Treatment options range from no treatment for a mild cystocele to surgery for a more extensive cystocele. If a cystocele is not bothersome, the clinician may only recommend avoiding heavy lifting or straining that could cause the cystocele to worsen. If symptoms are moderately bothersome, the doctor may recommend a pessary, a device placed in the vagina to hold the bladder in place. Treatment can consist of a combination of non-surgical and surgical management. Treatment choice is also related to age, desire to have children, severity of impairment, desire to continue sexual intercourse and other diseases that a woman may have.

Cystocele is often treated by non-surgical means:

- Pessary - This is a removable device inserted into the vagina to support the anterior vaginal wall. Pessaries come in many different shapes and sizes. There are sometimes complications with the use of a pessary.

- Pelvic floor muscle therapy - Pelvic floor exercises to strengthen vaginal support can be of benefit. Specialized physical therapy can be prescribed to help strengthen the pelvic floor muscles.

- Dietary changes - Ingesting high fiber foods will aid in promoting bowel movements.

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.

The principal treatment of chordee is surgery in infancy, usually by a pediatric urologist. With chordees caused by circumcision, the preferred method of surgical treatment is a z-plasty. The preferred time for surgery is between the ages of 6 and 18 months and correction is usually successful.

The main treatment for isolated epispadias is a comprehensive surgical repair of the genito-urinary area usually during the first 7 years of life, including reconstruction of the urethra, closure of the penile shaft and mobilisation of the corpora. The most popular and successful technique is known as the modified Cantwell-Ransley approach. In recent decades however increasing success has been achieved with the complete penile disassembly technique despite its association with greater and more serious risk of damage.

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.

If suspected antenatally, a consultation with a paediatric surgeon/ paediatric urologist maybe indicated to evaluate the risk and consider treatment options.

Treatment is by endoscopic valve ablation. Fetal surgery is a high risk procedure reserved for cases with severe oligohydramnios, to try to limit the associated lung underdevelopment, or pulmonary hypoplasia, that is seen at birth in these patients. The risks of fetal surgery are significant and include limb entrapment, abdominal injury, and fetal or maternal death. Specific procedures for "in utero" intervention include infusions of amniotic fluid, serial bladder aspiration, and creating a connection between the amniotic sac and the fetal bladder, or vesicoamniotic shunt.

There are three specific endoscopic treatments of posterior urethral valves:

- Vesicostomy followed by valve ablation - a stoma, or hole, is made in the urinary bladder, also known as "low diversion", after which the valve is ablated and the stoma is closed.

- Pyelostomy followed by valve ablation - stoma is made in the pelvis of the kidney as a slightly "high diversion", after which the valve is ablated and the stoma is closed

- Primary (transurethral) valve ablation - the valve is removed through the urethra without creation of a stoma

The standard treatment is primary (transurethral) ablation of the valves. Urinary diversion is used in selected cases, and its benefit is disputed.

Following surgery, the follow-up in patients with posterior urethral valve syndrome is long term, and often requires a multidisciplinary effort between paediatric surgeons/ paediatric urologists, pulmonologists, neonatologists, radiologists and the family of the patient. Care must be taken to promote proper bladder compliance and renal function, as well as to monitor and treat the significant lung underdevelopment that can accompany the disorder. Definitive treatment may also be indicated for the vesico-ureteral reflux.

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.

Paraphimosis can be avoided by bringing the foreskin back into its normal, forward, non-retracted position after retraction is no longer necessary (for instance, after cleaning the glans penis or placing a Foley catheter). Phimosis (both pathologic and normal childhood physiologic forms) is a risk factor for paraphimosis; "physiologic" phimosis resolves naturally as a child matures, but it may be advisable to treat "pathologic" phimosis via long-term stretching or elective surgical techniques (such as preputioplasty to loosen the preputial orifice or circumcision to amputate the foreskin tissue partially or completely).

The foreskin responds to the application of tension to cause expansion by creating new skin cells though the process of mitosis. The tissue expansion is permanent. Non-surgical stretching of the foreskin may be used to widen a narrow, non-retractable foreskin. Stretching may be combined with the use of a steroid cream. Beaugé recommends manual stretching for young males in preference to circumcision as a treatment for non-retractile foreskin because of the preservation of sexual sensation.

Paraphimosis can often be effectively treated by manual manipulation of the swollen foreskin tissue. This involves compressing the glans and moving the foreskin back to its normal position, perhaps with the aid of a lubricant, cold compression, and local anesthesia as necessary. If this fails, the tight edematous band of tissue can be relieved surgically with a dorsal slit or circumcision. An alternative method, the Dundee technique, entails placing multiple punctures in the swollen foreskin with a fine needle, and then expressing the edema fluid by manual pressure. According to Ghory and Sharma, treatment by circumcision may be elected as "a last resort, to be performed by a urologist". Other experts recommend delaying elective circumcision until after paraphimosis has been resolved.

Permanent stents are often metal coils, which are inserted into the male urethra. The braided mesh is designed to expand radially, applying constant gentle pressure to hold open the sections of the urethra that obstruct the flow of urine. The open, diamond-shape cell design of the stent allows the stent to eventually become embedded in the urethra, thus minimizing the risk for encrustation and migration. Permanent stents are used to relieve urinary obstructions secondary to benign prostatic hyperplasia (BPH), recurrent bulbar urethral stricture (RBUS), or detrusor external sphincter dyssynergia (DESD). The main motive for removal of permanent stents is worsening of symptoms even with device fitted. Other reasons have been migration, clot retention, hematuria, and urinary retention. The only FDA approved permanent stent is the Urolume. Usually, permanent stents are used only for men who are unwilling or unable to take medications or who are reluctant or unable to have surgery. Most doctors do not consider permanent stents a viable long-term treatment for most men.

The primary treatment for urethral diverticulum is surgical. The surgery is conducted transvaginally, usually when there is no acute inflammation to better aid dissection of the delicate tissues.

Hormones potentially increase the size of the penis, and have been used in children with proximal hypospadias who have a smaller penis. Numerous articles report testosterone injections or topical creams increase the length and circumference of the penis. However, few studies discuss the impact of this treatment on the success of corrective surgery, with conflicting results. Therefore, the role, if any, for preoperative hormone stimulation is not clear at this time.

A permanent urethral stent was approved for use in men with bulbar urethral strictures in 1996, but was recently removed from the market.

A temporary thermoexpandable urethral stent (Memotherm) is available in Europe, but is not currently approved for use in the United States.

In females, meatal stenosis can usually be treated in the physician's office using local anesthesia to numb the area and dilating (widening) the urethral opening with special instruments.

In boys, it is treated by a second surgical procedure called meatotomy in which the meatus is crushed with a straight mosquito hemostat and then divided with fine-tipped scissors. Recently, home-dilatation has been shown to be a successful treatment for most boys.

A number of medications exist to treat incontinence including: fesoterodine, tolterodine and oxybutynin. While a number appear to have a small benefit, the risk of side effects are a concern. For every ten or so people treated only one will become able to control their urine and all medication are of similar benefit.

Medications are not recommended for those with stress incontinence and are only recommended in those who have urge incontinence who do not improve with bladder training.

The treatment depends on the cause. Medications may work for retrograde ejaculation but only in a few cases. Surgery rarely is the first option for retrograde ejaculation and the results have proven to be inconsistent. Medications do not help retrograde ejaculation if there has been permanent damage to the prostate or the testes from radiation. Medications also do not help if prostate surgery has resulted in damage to the muscles or nerves. Medications only work if there has been mild nerve damage caused by diabetes, multiple sclerosis or mild spinal cord injury.

Hypospadias repair can be done in full-term, healthy infants at any time from 3 months of age. Premature babies generally have surgery done at 6 months or older. Using these guidelines, most babies can undergo repair as same-day surgery, without need to stay in the hospital afterwards.

The results of surgery are probably not influenced by the age at which repair is done, but older children are more likely to recall the event. Teens and adults typically spend one night in the hospital after surgery.

Surgery may be used to help stress or overflow incontinence. Common surgical techniques for stress incontinence include slings, tension-free vaginal tape, and bladder suspension among others. Urodynamic testing seems to confirm that surgical restoration of vault prolapse can cure motor urge incontinence. In those with problems following prostate surgery there is little evidence regarding the use of surgery.

A pessary is a medical device that is inserted into the vagina. The most common kind is ring shaped, and is typically recommended to correct vaginal prolapse. The pessary compresses the urethra against the symphysis pubis and elevates the bladder neck. For some women this may reduce stress leakage, however it is not clear how well these mechanical devices help women with stress urinary incontinence. If a pessary is used, vaginal and urinary tract infections may occur and regular monitoring by a doctor is recommended.

These medications tighten the bladder neck muscles and prevent semen from going backwards into the bladder. However, the medications do have many side effects and they have to be taken at least 1–2 hours prior to sexual intercourse. In many cases, the medications fail to work at the right time because most men are not able to predict when they will have an orgasm.

Brief doses of electrical stimulation can strengthen muscles in the lower pelvis in a way similar to exercising the muscles. Electrodes are temporarily placed in the vagina or rectum to stimulate nearby muscles. This can stabilize overactive muscles and stimulate contraction of urethral muscles.

Clinical research published in the British Medical Journal compared pelvic floor exercises, vaginal weights and electro-stimulation in a randomised trial. The research recommended that pelvic floor exercise should be the first choice of treatment for genuine stress incontinence because simple exercises proved to be far more effective than electro-stimulation or vaginal cones.

This situation was confirmed in a comprehensive review of the treatment of stress incontinence published in the British Journal of Urology International in 2010. The report author noted that electrical stimulation devices and weighted vaginal cones are not recommended by the UK National Institute for Clinical Excellence (NICE) and "are not universally advocated by clinicians as they have yet to produce sufficient evidence of efficacy".

Antimuscarinics such as tolterodine may also be used, especially in combination with alpha blockers. They act by decreasing acetylcholine effects on the smooth muscle of the bladder, thus helping control symptoms of an overactive bladder.

Phosphodiesterase-5 inhibitors such as sildenafil citrate show some symptomatic relief, suggesting a possible common cause with erectile dysfunction. Tadalafil was considered then rejected by NICE in the UK for the treatment of symptoms associated with BPH. In 2011, the U.S. Food and Drug Administration approved tadalafil to treat the signs and symptoms of benign prostatic hyperplasia, and for the treatment of BPH and erectile dysfunction (ED), when the conditions occur simultaneously.

The 5α-reductase inhibitors finasteride and dutasteride may also be used in men with BPH. These medications inhibit the 5α-reductase enzyme, which, in turn, inhibits production of DHT, a hormone responsible for enlarging the prostate. Effects may take longer to appear than alpha blockers, but they persist for many years. When used together with alpha blockers, no benefit was reported in short-term trials, but in a longer term study (3–4 years) there was a greater reduction in BPH progression to acute urinary retention and surgery than with either agent alone, especially in patients were more severe symptoms and larger prostates. Other trials have confirmed reductions in symptoms, within 6 months in one trial, an effect that was maintained after withdrawal of the alpha blocker. Side effects include decreased libido and ejaculatory or erectile dysfunction. The 5α-reductase inhibitors are contraindicated in pregnant women because of their teratogenicity due to interference with fetal testosterone metabolism, and as a precaution, pregnant women should not handle crushed or broken tablets.

Penile fracture is a medical emergency, and emergency surgical repair is the usual treatment. Delay in seeking treatment increases the complication rate. Non-surgical approaches result in 10–50% complication rates including erectile dysfunction, permanent penile curvature, damage to the urethra and pain during sexual intercourse, while operatively treated patients experience an 11% complication rate.

In some cases, retrograde urethrogram may be performed to rule out concurrent urethral injury.

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.