Treatment is typically with the antibiotics metronidazole or clindamycin. They can be either given by mouth or applied inside the vagina. About 10% to 15% of people, however, do not improve with the first course of antibiotics and recurrence rates of up to 80% have been documented. Recurrence rates are increased with sexual activity with the same pre-/posttreatment partner and inconsistent condom use although estrogen-containing contraceptives decrease recurrence. When clindamycin is given to pregnant women symptomatic with BV before 22 weeks of gestation the risk of pre-term birth before 37 weeks of gestation is lower.

Other antibiotics that may work include macrolides, lincosamides, nitroimidazoles, and penicillins.

Bacterial vaginosis is not considered a sexually transmitted infection, and treatment of a male sexual partner of a woman with bacterial vaginosis is not recommended.

A 2009 Cochrane review found tentative but insufficient evidence for probiotics as a treatment for BV. A 2014 review reached the same conclusion. A 2013 review found some evidence supporting the use of probiotics during pregnancy. The preferred probiotics for BV are those containing high doses of lactobacilli (around 10 ) given in the vagina. Intravaginal administration is preferred to taking them by mouth. Prolonged repetitive courses of treatment appear to be more promising than short courses.

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.

The cause of the infection determines the appropriate treatment. It may include oral or topical antibiotics and/or antifungal creams, antibacterial creams, or similar medications. A cream containing cortisone may also be used to relieve some of the irritation. If an allergic reaction is involved, an antihistamine may also be prescribed. For women who have irritation and inflammation caused by low levels of estrogen (postmenopausal), a topical estrogen cream might be prescribed.

The following are typical treatments for trichomoniasis, bacterial vaginosis, and yeast infections:

- Trichomoniasis: Single oral doses of either metronidazole, or tinidazole. "Sexual partner(s) should be treated simultaneously. Patients should be advised to avoid sexual intercourse for at least 1 week and until they and their partner(s) have completed treatment and follow-up."

- Bacterial vaginosis: The most commonly used antibiotics are metronidazole, available in both pill and gel form, and clindamycin available in both pill and cream form.

- Yeast infections: Local azole, in the form of ovula and cream. All agents appear to be equally effective. These anti-fungal medications, which are available in over the counter form, are generally used to treat yeast infections. Treatment may last anywhere between one, three, or seven days.

Up to 40% of women seek alternatives to treat vaginal yeast infection. Example products are herbal preparations, probiotics and vaginal acidifying agents. Other alternative treatment approaches include switching contraceptive, treatment of the sexual partner and gentian violet. However, the effectiveness of such treatments has not received much study.

Probiotics (either as pills or as yogurt) do not appear to decrease the rate of occurrence of vaginal yeast infections. No benefit has been found for active infections. Example probiotics purported to treat and prevent candida infections are Lactobacillus fermentum RC-14, Lactobacillus fermentum B-54, Lactobacillus rhamnosus GR-1, Lactobacillus rhamnosus GG and Lactobacillus acidophilus.

There is no evidence to support the use of special cleansing diets and colonic hydrotherapy for prevention.

Treatment can include topical steroids to diminish the inflammation. Antibiotics to diminish the proportion of aerobic bacteria is still a matter of debate. The use of local antibiotics, preferably local non-absorbed and broad spectrum, covering enteric gram-positive and gram-negative aerobes, can be an option. In some cases, systemic antibiotics can be helpful, such as amoxicillin/clavulanate or moxifloxacin. Vaginal rinsing with povidone iodine can provide relief of symptoms but does not provide long-term reduction of bacterial loads. Dequalinium chloride can also be an option for treatment.

The following treatments are typically recommended:

- Intravaginal agents: butoconazole, clotrimazole, miconazole, nystatin, tioconazole, terconazole. Candidal vulvovaginitis in pregnancy should be treated with intravaginal clotrimazole or nystatin for at least 7 days. All are more or less equally effective.

- By mouth: fluconazole as a single dose. For severe disease another dose after 3 days may be used.

Short-course topical formulations (i.e., single dose and regimens of 1–3 days) effectively treat uncomplicated candidal vulvovaginitis. The topically applied azole drugs are more effective than nystatin. Treatment with azoles results in relief of symptoms and negative cultures in 80–90% of patients who complete therapy.

The creams and suppositories in this regimen are oil-based and might weaken latex condoms and diaphragms. Treatment for vagina thrush using antifungal medication is ineffective in up to 20% of cases. Treatment for thrush is considered to have failed if the symptoms do not clear within 7–14 days. There are a number of reasons for treatment failure. For example, if the infection is a different kind, such as bacterial vaginosis (the most common cause of abnormal vaginal discharge), rather than thrush.

"C. trachomatis" infection can be effectively cured with antibiotics. Guidelines recommend azithromycin, doxycycline, erythromycin, levofloxacin or ofloxacin. Agents recommended during pregnancy include erythromycin or amoxicillin.

An option for treating sexual partners of those with chlamydia or gonorrhea include patient-delivered partner therapy (PDT or PDPT), which is the practice of treating the sex partners of index cases by providing prescriptions or medications to the patient to take to his/her partner without the health care provider first examining the partner.

Following treatment people should be tested again after three months to check for reinfection.

Treatment for TOA differs from PID in that some clinicians recommend patients with tubo-ovarian abscesses have at least 24 hours of inpatient parenteral treatment with antibiotics, and that they may require surgery. If surgery becomes necessary, pre-operative administration of broad-spectrum antibiotics is started and removal of the abscess, the affected ovary and fallopian tube is done. After discharge from the hospital, oral antibiotics are continued for the length of time prescribed by the physician.

Treatment is different if the TOA is discovered before it ruptures and can be treated with IV antibiotics. During this treatment, IV antibiotics are usually replaced with oral antibiotics on an outpatient basis. Patients are usually seen three days after hospital discharge and then again one to two weeks later to confirm that the infection has cleared. Ampicillin/sulbactam plus doxycycline is effective against C. trachomatis, N. gonorrhoeae, and anaerobes in women with tubo-ovarian abscess. Parenteral Regimens described by the Centers for Disease Control and prevention are Ampicillin/Sulbactam 3 g IV every 6 hours and Doxycycline 200 mg orally or IV every 24 hours, though other regiemes that are used for pelvic inflammatory disease have been effective.

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.

Treatment is often started without confirmation of infection because of the serious complications that may result from delayed treatment. Treatment depends on the infectious agent and generally involves the use of antibiotic therapy. If there is no improvement within two to three days, the patient is typically advised to seek further medical attention. Hospitalization sometimes becomes necessary if there are other complications. Treating sexual partners for possible STIs can help in treatment and prevention.

For women with PID of mild to moderate severity, parenteral and oral therapies appear to be effective. It does not matter to their short- or long-term outcome whether antibiotics are administered to them as inpatients or outpatients. Typical regimens include cefoxitin or cefotetan plus doxycycline, and clindamycin plus gentamicin. An alternative parenteral regimen is ampicillin/sulbactam plus doxycycline. Erythromycin-based medications can also be used. Another alternative is to use a parenteral regimen with ceftriaxone or cefoxitin plus doxycycline. Clinical experience guides decisions regarding transition from parenteral to oral therapy, which usually can be initiated within 24–48 hours of clinical improvement.

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.

Urinary catheters should be inserted using aseptic technique and sterile equipment (including sterile gloves, drape, sponges, antiseptic and sterile solution), particularly in an acute care setting. Hands should be washed before and after catheter insertion. Overall, catheter use should be minimized in all patients, particularly those at higher risk of CAUTI and mortality (e.g. the elderly or those with impaired immunity).

Complications of TOA are related to the possible removal of one or both ovaries and fallopian tubes. Without these reproductive structures, fertility can be affected. Surgical complications can develop and include:

- Allergic shock due to anesthetics

- A paradoxical reaction to a drug

- Infection

Treatment is not usually necessary in asymptomatic cases, since most fusions will separate naturally over time, but may be required when symptoms are present. The standard method of treatment for labial fusion is the application of topical estrogen cream onto the areas of adhesion, which is effective in 90% of patients. In severe cases where the labia minora are entirely fused, causing urinary outflow obstruction or vaginal obstruction, the labia should be separated surgically. Recurrence after treatment is common but is thought to be prevented by good hygiene practices. One study has shown that betamethasone may be more effective than estrogen cream in preventing recurrence, with fewer side effects.

In both the acute and chronic forms, antibiotics are used if an infection is suspected. The treatment of choice is often azithromycin and cefixime to cover both gonorrhoeae and chlamydia. Fluoroquinolones are no longer recommended due to widespread resistance of gonorrhoeae to this class. Doxycycline may be used as an alternative to azithromycin. In chronic epididymitis, a four- to six-week course of antibiotics may be prescribed to ensure the complete eradication of any possible bacterial cause, especially the various chlamydiae.

For cases caused by enteric organisms (such as "E. coli"), ofloxacin or levofloxacin are recommended.

In children, fluoroquinolones and doxycycline are best avoided. Since bacteria that cause urinary tract infections are often the cause of epididymitis in children, co-trimoxazole or suited penicillins (for example, cephalexin) can be used.

Household remedies such as elevation of the scrotum and cold compresses applied regularly to the scrotum may relieve the pain in acute cases. Painkillers or anti-inflammatory drugs are often used for treatment of both chronic and acute forms. Hospitalisation is indicated for severe cases, and check-ups can ensure the infection has cleared up. Surgical removal of the epididymis is rarely necessary, causes sterility, and only gives relief from pain in approximately 50% of cases. However, in acute suppurating epididymitis (acute epididymitis with a discharge of pus), a epididymotomy may be recommended; in refractory cases, a full epididymectomy may be required. In cases with unrelenting testicular pain, removal of the entire testicle—orchiectomy—may also be warranted.

It is generally believed that most cases of chronic epididymitis will eventually "burn out" of patient's system if left untreated, though this might take years or even decades. However, some prostate-related medications have proven effective in treating chronic epididymitis, including doxazosin.

Neonatal infection treatment is typically started before the diagnosis of the cause can be confirmed.

Neonatal infection can be prophylactically treated with antibiotics. Maternal treatment with antibiotics is primarily used to protect against group B streptococcus.

Women with a history of HSV, can be treated with antiviral drugs to prevent symptomatic lesions and viral shedding that could infect the infant at birth. The antiviral medications used include acyclovir, penciclovir, valacyclovir, and famciclovir. Only very small amounts of the drug can be detected in the fetus. There are no increases in drug-related abnormalities in the infant that could be attributed to acyclovir. Long-term effects of antiviral medications have not been evaluated for their effects after growth and development of the child occurs. Neutropenia can be a complication of acyclovir treatment of neonatal HSV infection, but is usually transient. Treatment with immunoglobulin therapy has not been proven to be effective.

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.

Even when the PID infection is cured, effects of the infection may be permanent. This makes early identification essential. Treatment resulting in cure is very important in the prevention of damage to the reproductive system. Formation of scar tissue due to one or episodes of PID can lead to tubal blockage, increasing the risk of the inability to get pregnant and long-term pelvic/abdominal pain. Certain occurrences such as a post pelvic operation, the period of time immediately after childbirth (postpartum), miscarriage or abortion increase the risk of acquiring another infection leading to PID.

"Actinomyces" bacteria are generally sensitive to penicillin, which is frequently used to treat actinomycosis. In cases of penicillin allergy, doxycycline is used.

Sulfonamides such as sulfamethoxazole may be used as an alternative regimen at a total daily dosage of 2-4 grams. Response to therapy is slow and may take months.

Hyperbaric oxygen therapy may also be used as an adjunct to conventional therapy when the disease process is refractory to antibiotics and surgical treatment.

Use of vaginally administered estrogens (including vaginal tablets or cream) is appropriate before the condition becomes severe. Regular sexual activity may be helpful. A water-soluble vaginal lubricant can be helpful in mild cases.

Increasingly, vaginally administered estrogens based on low dose of estriol are used to stimulate the vaginal epithelium proliferation. There is growing evidence to support the use of both Fractional Erbium and Fractional CO2 laser therapy, both have proven to be an effective treatment strategy, especially for patients such as cancer survivors for whom vaginal estrogen is not always an option. The characteristic of both Erbium and CO2 laser wavelengths is that they are highly absorbed within water. It is the water within the sub mucosa that is targeted by the laser. The hypothesised mode of action for Erbium laser is that through selectively heating the submucosa a process of neocollagenesis and neo vascularisation occurs. This can lead to an improvement of the blood flow and overall health of the treated area. Treatments take approximately 20 minutes and can be performed within an outpatient setting.

For fallopian tube obstruction, alternative medicine has been used as a form of fertility treatment. A study of the use of alternative methods showed that only a minority of infertile couples utilize such treatments. It also showed that alternative methods are more often chosen by couples who were wealthier, have not yet achieved pregnancy, or had a belief in the effectiveness of such treatments. Of the study participants, 29% used a CAM modality for treatment, 22% used acupuncture, 17% used herbal therapies like Fuyan Pill, and 1% using meditation.