Your ovaries may hurt during your period because you are suffering from ovarian cysts. Symptoms of ovarian cysts include menstrual irregularities, pelvic pain, pain in your ovaries during your period, pain in your ovaries right before your period, pain during intercourse, and pain during bowel movements. An ovarian cyst may form around the midpoint of a woman's menstrual cycle. It will form when an egg isn't released as it should. Some medications that is used to induce ovulation can also increase the chances of ovarian cysts forming.