Im 13 and why do my knees thighs and ankles hurt when I run?

They hurt because running is a physical activity and you are probably out of shape. Keep running and over time it will stop hurting.

A different point of view...At 13, your body is undergoing a lot of growth. The areas you described are high stress areas, and they hurt adult runners as well. In your case, the pain may reflect both the normal stress runners feel performing this activity, as well as pains associated with your high rate of growth. It doesn't sound as if being out of shape has anything to do with this.