I have a male best friend. He’s always been in love with me but I was in a relationship and that created some distance . I broke off my relationship due to some issues and we became quite close again.
But then I thought he was over me but suddenly he’s seeing this girl and they are dating. We both lost our virginity to each other and he keeps saying he wishes he could be with me. I can’t stand him dating her and I think I should break things off with him. We still have sex often, even though he now has a girlfriend. I’m just confused on what to do.
LemonVibe 
This post is very ambiguous. Almost sounds like this could be a woman writing this story.
Either way, I’d say break it off. You’re the person on the side. It’s demoralizing. You shouldn’t let yourself be used for sex when he’s tired of his girlfriend. End things.
Oh, sorry about that! After reading the question again, I’m pretty sure this is a woman. I’ve revised the title accordingly.
Oh that sounds awful. You need a significant amount of space from each other. You may always have feelings for one another, but some time will help you guys think clearer. But I have to beg the question, if you like him and he likes you, why aren’t you two together?