I have pcos and lately it has been painful to have sex. could this be a cyst?

Could be. See an OB: Pain with sex could be due to an ovarian cyst, an infection such as pid, bladder infection, endometriosis, fibroids, adenomyosis, or scar tissue. See your ob/gyn for a checkup, especially if you are having fevers or abnormal discharge. Polycystic ovarian syndrome (pcos) affects about 8-10% of women and doesn't cause pelvic pain by itself.