Sometimes, birth control pills help migraines. Sometimes, they make headaches worse. How birth control affects migraines depends on the woman and on the level of hormones present in the pill she takes. A drop in estrogen levels can trigger migraines. That’s why some women get headaches just before their period, which is when estrogen levels dip. If you have these menstrual migraines, birth control pills might help prevent your headaches by keeping your estrogen levels stable throughout the menstrual cycle.