Hi Rexter! Welcome to the forum.
I assume it's not sprained or a stress fracture from a previous injury, it sounds like you'd know if that was the case.
Does the ankle pain come on at the beginning of your run, then go away, and only return after your run? Does it hurt up the back of your leg as well? If so, it could be tendinitis. Reduce inflammation with ice, NSAIDs, and gentle stretching, and try to find a softer running surface for a while, see if that makes a difference.