Treatment is directed at the underlying condition and usually surgical.

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.

Hematosalpinx (sometimes also hemosalpinx) is a medical condition involving bleeding into the fallopian tubes.

Ectopic gestation exists in mammals other than humans. In sheep, it can go to term, with mammary preparation to parturition, and expulsion efforts. The fetus can be removed by cesarian section. Pictures of cesarian section of a euthanized ewe, 5 days after parturition signs.

Salpingectomy as a treatment for ectopic pregnancy is one of the common cases when the principle of double effect can be used to justify accelerating the death of the embryo by doctors and patients opposed to outright abortions.

In the Catholic church, there are moral debates on certain treatments. A significant number of Catholic moralists consider use of methotrexate and the salpingostomy procedure to be not "morally permissible" because they destroy the embryo; however situations are considered differently in which the mother's health is endangered, and the whole fallopian tube with the developing embryo inside is removed.

A simple cruciate incision followed by excision of tags of hymen allows drainage of the retained menstrual blood. A thicker transverse vaginal septum can be treated with Z-plasty. A blind vagina will require a partial or complete vaginoplasty. Hematosalpinx may require laprotomy or laparoscopy for removal and reconstruction of affected tube.

Infertility may require assisted reproductive techniques.

The first line of therapy after diagnosis typically involves the administration of the combined oral contraceptive pill, medroxyprogesterone acetate or a gonadotropin-releasing hormone agonist to suppress menstruation and thereby relieve pain. Surgically, cervical agenesis has historically been treated through hysterectomy (removal of the uterus) to relieve symptoms caused by hematocolpos (the accumulation of menstrual fluid in the vagina). Other surgical methods of management involve the creation of an anastomotic connection between the uterus and vagina by neovaginoplasty or recanalization of the cervix. Outcomes in these cases are generally poor, since the natural functions of the cervix—such as mucus production and providing a barrier against ascending infection—cannot be replicated. Furthermore, the success rate of uterovaginal anastomosis is less than 50% and most patients require multiple surgeries while many develop cervical stenotis. Despite this, several pregnancies have been reported in women with cervical agenesis who underwent surgical treatment.

Cryptomenorrhea or cryptomenorrhoea, also known as hematocolpos, is a condition where menstruation occurs but is not visible due to an obstruction of the outflow tract. Specifically the endometrium is shed, but a congenital obstruction such as a vaginal septum or on part of the hymen retains the menstrual flow. A patient with cryptomenorrhea will appear to have amenorrhea but will experience cyclic menstrual pain. The condition is surgically correctable.

The patient usually presents at the age of puberty when the commencement of menstruation blood gets collected in the vagina and gives rise to symptoms.

Cervical agenesis is estimated to occur in 1 in 80,000 females. It is often associated with deformity of the vagina; one study found that 48% of patients with cervical agenesis had a normal, functional vagina, while the rest of the cases were accompanied by vaginal hypoplasia.