Sex hurts :(

My boyfriend and I have known each other for about 6 months now. We’ve recently started dating and he was my first. We used to go at it every time we saw each other. But recently he was going at it and he helped during by touching my clitoris, when it was starting to become painful. Since then sex has become painful near the bottom half of my vagina. I’ve even cried in front of him because of the pain. He totally understood and stopped when I said so. We took a break from sex and even more time passed by since I have gotten my period. I just finished and we tried to have sex again. We got in the mood and even though it felt good at first, the more we kept going the more it hurt. It makes me sad because I know he wants to pleasure me as well as himself but we can’t because I am hurting. The gynecologist told me I don’t have any type of std, so what could I do to make it stop hurting?