A number of medications can be used to treat this disorder. Alpha blockers and/or antibiotics appear to be the most effective with NSAIDs such as ibuprofen providing lesser benefit.

- Treatment with antibiotics is controversial. Some have found benefits in symptoms while others have questioned the utility of a trial of antibiotics. Antibiotics are known to have anti-inflammatory properties and this has been suggested as an explanation for their partial efficacy in treating CPPS. Antibiotics such as fluoroquinolones, tetracyclines, and macrolides have direct anti-inflammatory properties in the absence of infection, blocking inflammatory chemical signals (cytokines) such as interleukin-1 (IL-1), interleukin-8 and tumor necrosis factor (TNF), which coincidentally are the same cytokines found to be elevated in the semen and EPS of men with chronic prostatitis.

- The effectiveness of alpha blockers (tamsulosin, alfuzosin) is questionable in men with CPPS. A 2006 meta-analysis found that they are moderately beneficial when the duration of therapy was at least 3 months.

- An estrogen reabsorption inhibitor such as mepartricin improves voiding, reduces urological pain and improves quality of life in patients with chronic non-bacterial prostatitis.

- Therapies that have not been properly evaluated in clinical trials although there is supportive anecdotal evidence include gabapentin, benzodiazepines, and amitriptyline.

Category III prostatitis may have no initial trigger other than anxiety, often with an element of OCD, panic disorder, or other anxiety-spectrum problem. This is theorized to leave the pelvic area in a sensitized condition resulting in a loop of muscle tension and heightened neurological feedback (neural pain wind-up). Current protocols largely focus on stretches to release overtensed muscles in the pelvic or anal area (commonly referred to as trigger points) including digital intrarectal massage, physical therapy to the area, and progressive relaxation therapy to reduce causative stress.

Aerobic exercise can help those sufferers who are not also suffering from chronic fatigue syndrome or whose symptoms are not exacerbated by exercise. Acupuncture has reportedly benefited some patients.

For chronic nonbacterial prostatitis (Cat III), also known as CP/CPPS, which makes up the majority of men diagnosed with "prostatitis", a treatment called the "Wise–Anderson Protocol" (aka the "Stanford Protocol"), has recently been published. This is a combination of:

- Medication (using tricyclic antidepressants and benzodiazepines)

- Psychological therapy (paradoxical relaxation, an advancement and adaptation, specifically for pelvic pain, of a type of progressive relaxation technique developed by Edmund Jacobson during the early 20th century)

- Physical therapy (trigger point release therapy on pelvic floor and abdominal muscles, and also yoga-type exercises with the aim of relaxing pelvic floor and abdominal muscles).

Biofeedback physical therapy to relearn how to control pelvic floor muscles may be useful. Biofeedback is satisfactory for treatment of chronic prostatitis (with mainly voiding problems) during puberty.

Diet modification is often recommended as a first-line method of self-treatment for interstitial cystitis, though rigorous controlled studies examining the impact diet has on interstitial cystitis signs and symptoms are currently lacking. Individuals with interstitial cystitis often experience an increase in symptoms when they consume certain foods and beverages. Avoidance of these potential trigger foods and beverages such as caffeine-containing beverages including coffee, tea, and soda, alcoholic beverages, chocolate, citrus fruits, hot peppers, and artificial sweeteners may be helpful in alleviating symptoms. Diet triggers vary between individuals with IC; the best way for a person to discover his or her own triggers is to use an elimination diet. Sensitivity to trigger foods may be reduced if calcium glycerophosphate and/or sodium bicarbonate is consumed. The foundation of therapy is a modification of diet to help patients avoid those foods which can further irritate the damaged bladder wall.

The mechanism by which dietary modification benefits people with IC is unclear. Integration of neural signals from pelvic organs may mediate the effects of diet on symptoms of IC.

Bladder instillation of medication is one of the main forms of treatment of interstitial cystitis, but evidence for its effectiveness is currently limited. Advantages of this treatment approach include direct contact of the medication with the bladder and low systemic side effects due to poor absorption of the medication. Single medications or a mixture of medications are commonly used in bladder instillation preparations. DMSO is the only approved bladder instillation for IC/BPS yet it is much less frequently used in urology clinics.

A 50% solution of DMSO had the potential to create irreversible muscle contraction. However, a lesser solution of 25% was found to be reversible. Long-term use of DMSO is questionable, as its mechanism of action is not fully understood though DMSO is thought to inhibit mast cells and may have anti-inflammatory, muscle-relaxing, and analgesic effects. Other agents used for bladder instillations to treat interstitial cystitis include: heparin, lidocaine, chondroitin sulfate, hyaluronic acid, pentosan polysulfate, oxybutynin, and botulinum toxin A. Preliminary evidence suggests these agents are efficacious in reducing symptoms of interstitial cystitis, but further study with larger, randomized, controlled clinical trials is needed.

Trigonitis is a condition of inflammation of the trigone region of the bladder. It is more common in women.

The cause of trigonitis is not known, and there is no solid treatment. Electrocautery is sometimes used, but is generally unreliable as a treatment, and typically does not have quick results. Several drugs, such as muscle relaxants, antibiotics, antiseptics such as Urised, have varied and unreliable results. Other forms of treatment include urethrotomy, cryosurgery, and neurostimulation.

People with acute pyelonephritis that is accompanied by high fever and leukocytosis are typically admitted to the hospital for intravenous hydration and intravenous antibiotic treatment. Treatment is typically initiated with an intravenous fluoroquinolone, an aminoglycoside, an extended-spectrum penicillin or cephalosporin, or a carbapenem. Combination antibiotic therapy is often used in such situations. The treatment regimen is selected based on local resistance data and the susceptibility profile of the specific infecting organism(s).

During the course of antibiotic treatment, serial white blood cell count and temperature are closely monitored. Typically, the intravenous antibiotics are continued until the person has no fever for at least 24 to 48 hours, then equivalent antibiotics by mouth can be given for a total of 2–week duration of treatment. Intravenous fluids may be administered to compensate for the reduced oral intake, insensible losses (due to the raised temperature) and vasodilation and to optimize urine output. Percutaneous nephrostomy or ureteral stent placement may be indicated to relieve obstruction caused by a stone. Children with acute pyelonephritis can be treated effectively with oral antibiotics (cefixime, ceftibuten and amoxicillin/clavulanic acid) or with short courses (2 to 4 days) of intravenous therapy followed by oral therapy. If intravenous therapy is chosen, single daily dosing with aminoglycosides is safe and effective.

Treatment of xanthogranulomatous pyelonephritis involves antibiotics as well as surgery. Removal of the kidney is the best surgical treatment in the overwhelming majority of cases, although polar resection (partial nephrectomy) has been effective for some people with localized disease. Watchful waiting with serial imaging may be appropriate in rare circumstances.

In people who do not require hospitalization and live in an area where there is a low prevalence of antibiotic-resistant bacteria, an fluoroquinolone by mouth such as ciprofloxacin or levofloxacin is an appropriate initial choice for therapy. In areas where there is a higher prevalence of fluoroquinolone resistance, it is useful to initiate treatment with a single intravenous dose of a long-acting antibiotic such as ceftriaxone or an aminoglycoside, and then continuing treatment with a fluoroquinolone. Oral trimethoprim/sulfamethoxazole is an appropriate choice for therapy if the bacteria is known to be susceptible. If trimethoprim/sulfamethoxazole is used when the susceptibility is not known, it is useful to initiate treatment with a single intravenous dose of a long-acting antibiotic such as ceftriaxone or an aminoglycoside. Oral beta-lactam antibiotics are less effective than other available agents for treatment of pyelonephritis. Improvement is expected in 48 to 72 hours.

Uncomplicated infections can be diagnosed and treated based on symptoms alone. Antibiotics taken by mouth such as trimethoprim/sulfamethoxazole (TMP/SMX), nitrofurantoin, or fosfomycin are typically first line. Cephalosporins, amoxicillin/clavulanic acid, or a fluoroquinolone may also be used. However, resistance to fluoroquinolones among the bacterial that cause urinary infections has been increasing. The FDA recommends against the use of fluoroquinolones when other options are available due to higher risks of serious side effects. These medications substantially shorten the time to recovery with all being equally effective. A three-day treatment with trimethoprim, TMP/SMX, or a fluoroquinolone is usually sufficient, whereas nitrofurantoin requires 5–7 days. Fosfomycin may be used as a single dose but has been associated with lower rates of efficacy.

With treatment, symptoms should improve within 36 hours. About 50% of people will recover without treatment within a few days or weeks. Fluoroquinolones are not recommended as a first treatment. The Infectious Diseases Society of America states this due to the concern of generating resistance to this class of medication. Amoxicillin-clavulanate appears less effective than other options. Despite this precaution, some resistance has developed to all of these medications related to their widespread use. Trimethoprim alone is deemed to be equivalent to TMP/SMX in some countries. For simple UTIs, children often respond to a three-day course of antibiotics. Women with recurrent simple UTIs may benefit from self-treatment upon occurrence of symptoms with medical follow-up only if the initial treatment fails.

The mainstay of treatment is antibiotics. Phenazopyridine is occasionally prescribed during the first few days in addition to antibiotics to help with the burning and urgency sometimes felt during a bladder infection. However, it is not routinely recommended due to safety concerns with its use, specifically an elevated risk of methemoglobinemia (higher than normal level of methemoglobin in the blood). Acetaminophen (paracetamol) may be used for fevers. There is no good evidence for the use of cranberry products for treating current infections.

Proper treatment of autonomic dysreflexia involves administration of anti-hypertensives along with immediate determination and removal of the triggering stimuli. Often, sitting the patient up and dangling legs over the bedside can reduce blood pressures below dangerous levels and provide partial symptom relief. Tight clothing and stockings should be removed. Straight catheterization of the bladder every 4 to 6 hrs, or relief of a blocked urinary catheter tube may resolve the problem. The rectum should be cleared of stool impaction, using anaesthetic lubricating jelly. If the noxious precipitating trigger cannot be identified, drug treatment is needed to decrease elevating intracranial pressure until further studies can identify the cause.

Drug treatment includes the rapidly acting vasodilators, including sublingual nitrates or oral clonidine. Ganglionic blockers are also used to control sympathetic nervous system outflow. Topical nitropaste is a convenient and safe treatment—an inch or two can be applied to the chest wall, and wiped off when blood pressures begin to normalize. Autonomic dysreflexia is abolished temporarily by spinal or general anaesthesia. These treatments are used during obstetric delivery of a woman with autonomic dysreflexia.

In a small minority of cases of urethral syndrome, treatment with antibiotics is effective, which indicates that in some cases it may be caused by bacterial infection which does not show up in either urinalysis or urine culture. For chronic urethral syndrome, a long term, low-dose antibiotic treatment is given on a continuous basis or after intercourse each time if intercourse appears to trigger symptoms.

As low oestrogen may also be considered a source for urethral syndrome, hormone replacement therapy, and oral contraceptive pill (birth-control pills) containing oestrogen are also used to treat the symptoms of this condition in women.

Treatment of TSP involves corticosteroids to help with inflammation. Though any success with corticosteroids is short-lived, with symptoms worsened as the dosage is reduced. A synthetic derivative, 17-alpha-ethinyltestosterone, can be used to treat Tropical spastic paraparesis, improvement in motor and bladder function was reported but not sustainable.

Mogamulizumab, an anti-CCR4 IgG1 monoclonal antibody, is also being researched as a possible treatment for Tropical spastic paraparesis. The antibody reduces HTLV-1 proviral load and production of proinflammatory cytokines. Valproic acid has also succeeded in reducing the proviral load of HTLV-1 (though clinical benefits were minimal or none). A further combination of valproic acid and zidovudine has demonstrated a decrease in proviral loads (in animals).

Unfortunately mesna is ineffective as a treatment once hemorrhagic cystitis has developed. Although rare, once a case of radiation-induced hemorrhagic cystitis is diagnosed there is no empirically-proven treatments to heal this type of condition, which can severely degrade a patient's quality of life and might possibly lead to renal failure with risk of death.

Viral hemorrhagic cystitis in children generally spontaneously resolves within a few days.

The first step in the treatment of HC should be directed toward clot evacuation. Bladder outlet obstruction from clots can lead to urosepsis, bladder rupture, and renal failure. Clot evacuation can be performed by placing a wide-lumen bladder catheter at bedside. The bladder can be irrigated with water or sodium chloride solution. The use of water is preferable because water can help with clot lysis. Care must be taken to not overdistend the bladder and cause a perforation.. Hyperbaric oxygen (HBO2) therapy has been proven to be effective in treating radiation-induced hemorrhagic cystitis.

Symptomatic bacteriuria is typically treated as a urinary tract infection with antibiotics. Common choices include nitrofurantoin, and trimethoprim/sulfamethoxazole.

Asymptomatic bacteriuria generally does not require treatment. Exceptions include during pregnancy and in those undergoing surgery of the urinary tract. Children with vesicoureteral reflux or others with structural abnormalities of the urinary tract.

There is no indication to treat asymptomatic bacteriuria in diabetics, renal transplant recipients, and in those with spinal cord injuries.

The overuse of antibiotic therapy to treat asymptomatic bacteriuria increases the risk of diarrhea, antimicrobial resistance, and infection due to Clostridium difficile. Other effects include increased financial burdens and overreporting of mandated catheter-associated urinary tract infection.

A number of antimuscarinic drugs (e.g., darifenacin, hyoscyamine, oxybutynin, tolterodine, solifenacin, trospium, fesoterodine) are frequently used to treat overactive bladder. β3 adrenergic receptor agonists (e.g., mirabegron), may be used, as well. They are, however, a second line treatment due to the risk of side effects.

Few people get complete relief with medications and all medications are no more than moderately effective.

A typical person with overactive bladder may urinate 12 times per day. Medication may reduce this number by 2-3 and reduce urinary incontinence events by 1-2 per day.

Various devices (Urgent PC Neuromodulation System) may also be used. Botulinum toxin A (Botox) is approved by the Food and Drug Administration in adults with neurological conditions, including multiple sclerosis and spinal cord injury. Botulinum Toxin A injections into the bladder wall can suppress involuntary bladder contractions by blocking nerve signals and may be effective for up to 9 months. The growing knowledge of pathophysiology of overactive bladder fuelled a huge amount of basic and clinical research in this field of pharmacotherapy. A surgical intervention involves the enlargement of the bladder using bowel tissues, although generally used as a last resort. This procedure can greatly enlarge urine volume in the bladder.

OAB may be treated with electrical stimulation, which aims to reduce the contractions of the muscle that tenses around the bladder and causes urine to pass out of it. There are invasive and non-invasive electrical stimulation options. Non-invasive options include the introduction of a probe into the vagina or anus, or the insertion of an electrical probe into a nerve near the ankle with a fine needle. These non-invasive options appear to reduce symptoms while they are in use, and are better than no treatment, or treatment with drugs, or pelvic floor muscle treatment, but the quality of evidence is low. It is unknown which electrical stimulation option works best. Also, it is unknown whether the benefits last after treatment stops.

Medical treatment entails low dose antibiotic prophylaxis until resolution of VUR occurs. Antibiotics are administered nightly at half the normal therapeutic dose. The specific antibiotics used differ with the age of the patient and include:

- Amoxicillin or ampicillin – infants younger than 6 weeks

- Trimethoprim-sulfamethoxazole (co-trimoxazole) – 6 weeks to 2 months

After 2 months the following antibiotics are suitable:

- Nitrofurantoin {5–7 mg/kg/24hrs}

- Nalidixic acid

- Bactrim

- Trimethoprim

- Cephalosporins

Urine cultures are performed 3 monthly to exclude breakthrough infection. Annual radiological investigations are likewise indicated. Good perineal hygiene, and timed and double voiding are also important aspects of medical treatment. Bladder dysfunction is treated with the administration of anticholinergics.

Even when caught early, aggressive treatment is required (Bobba). Antibiotics are proven to cure Emphysematous cystitis over time and reduce the amount of gas inside the bladder wall. Prognosis is poor if antibiotics are not used to treat the patient. Additional treatment consists of urinary drainage and good control of blood glucose. The treatment of underlying comorbid diseases, such as diabetes, is extremely important because they can intensify the infection (Gheonea, Bondari). Hyperbaric oxygen is an effective treatment, and has cured some cases in as little as 48 hours. Although it is unclear as to how gas formation occurs in emphysematous cystitis, it’s dependant on whether or not the patient has contributing diseases (Mccabe). Gas formation in diabetic patients diagnosed with Emphysematous cystitis has been determined to occur due to the production of carbon dioxide as a result of the fermentation of the high concentrations of glucose. Gas formation in nondiabetic patients is most likely due the breaking down of urinary lactulose and tissue proteins. Inflammation caused by infection increases pressure and decreases circulation, which provides the perfect environment for bacteria to produce gas (Sereno).

When in acute urinary retention, treatment of the urethral stricture or diversion is an emergency. Options include:

- Urethral dilatation and catheter placement. This can be performed in the Emergency Department, a practitioner's office or an operating room. The advantage of this approach is that the urethra may remain patent for a period of time after the dilation, though long-term success rates are low.

- Insertion of a suprapubic catheter with catheter drainage system. This procedure is performed in an Operating Room, Emergency Department or practitioner's office. The advantage of this approach is that it does not disrupt the scar and interfere with future definitive surgery.

Endoscopic injection involves applying a gel around the ureteral opening to create a valve function and stop urine from flowing back up the ureter. The gel consists of two types of sugar-based molecules called dextranomer and hyaluronic acid. Trade names for this combination include Deflux and Zuidex. Both constituents are well-known from previous uses in medicine. They are also biocompatible, which means that they do not cause significant reactions within the body. In fact, hyaluronic acid is produced and found naturally within the body.

Modification of predisposing factors can sometimes slow or reverse stone formation. Treatment varies by stone type, but, in general:

- Medication

- Surgery (lithotomy)

- Antibiotics and/or surgery for infections

- Medication

- Extracorporeal shock wave lithotripsy (ESWL) for removal of calculi

Catheterization methods range from intermittent catheterization, which involves no surgery or permanently attached appliances, to the creation of a stoma, which bypasses the urethra to empty the bladder directly.

Intermittent catheterization is the use, several times a day, of straight catheters (which are usually disposable or single-use products) to empty the bladder. This can be done independently by the patient, or with help, in the case that the patient lacks the dexterity to manage the catheter. For patients who are unable to tolerate disposable straight catheters, a Foley catheter allows continuous drainage of urine into a sterile drainage bag that is worn by the patient.

Other treatments involve creation of a stoma that is continent and readily accepts a catheter. These are known as Mitrofanoff mechanisms. An example of this treatment is the creation of an Indiana pouch. Additionally, a muscarinic agonist like Bethanechol may also be used, particularly in the postpartum or postoperative period. Function of the stoma may be augmented by periodic injections of botulinum toxin to relax one of the two sphincters involved in normal urination. The effect is longer-lasting with botulinum toxin type A than with type B. This use of botulinum toxin is discussed at length in the French medical literature.

Therapy for UAB is often dependent on factors such as age, health, symptoms, and cause of the condition. Treatment frequently includes lifestyle modification (fluid restriction, bladder retraining). Bethanechol is a prescription medication used for treatment, bethanechol can stimulate the nerves of the bladder, making them more responsive to stimulus. With UAB, it is common for patients to utilize a urinary catheter to void. Surgical options are also options, with a cuff or stent placed around or in the neck of the bladder to aid the emptying and leakage of urine. Neuromodulatory techniques such as sacral nerve or posterior tibial nerve stimulation may be of value in selected cases. However, current therapies are considered inadequate and there is a strong need for new research and attention.(Van Koeveringe et al., 2011; Tyagi et al. 2015).

Nighttime incontinence may be treated by increasing ADH levels. The hormone can be boosted by a synthetic version known as desmopressin, or DDAVP, which recently became available in pill form. Patients can also spray a mist containing desmopressin into their nostrils. Desmopressin is approved for use by children. There is difficulty in keeping the bed dry after medication is stopped, with as high as an 80% relapse rate.

Another medication, called imipramine, is also used to treat sleepwetting. It acts on both the brain and the urinary bladder. Unfortunately, total dryness with either of the medications available is achieved in only about 20 percent of patients.

If a young person experiences incontinence resulting from an overactive bladder, a doctor might prescribe a medicine that helps to calm the bladder muscle, such as oxybutynin. This medicine controls muscle spasms and belongs to a class of medications called anticholinergics.