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.

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

With the advent of IVF which bypasses the need for tubal function a more successful treatment approach has become available for women who want to conceive. IVF has now become the major treatment for women with hydrosalpinx to achieve a pregnancy.

Several studies have shown that IVF patients with untreated hydrosalpinx have lower conception rates than controls and it has been speculated that the tubal fluid that enters the endometrial cavity alters the local environment or affects the embryo in a detrimental way. Thus, many specialists advocate that prior to an IVF attempt, the hydrosalpinx should be removed.

For most of the past century patients with tubal infertility due to hydrosalpinx underwent tubal corrective surgery to open up the distally occluded end of the tubes (salpingostomy) and remove adhesions (adhesiolysis). Unfortunately, pregnancy rates tended to be low as the infection process often had permanently damaged the tubes, and in many cases hydrosalpinges and adhesions formed again. Further, ectopic pregnancy is a typical complication. Surgical interventions can be done by laparotomy or laparoscopy.

Non-infertile patients who suffer from severe chronic pain due to hydrosalpinx formation that is not relieved by pain management may consider surgical removal of the affected tube(s) (salpingectomy) or even a hysterectomy with removal of the tubes, possibly ovaries.