Ankle/Knee Pain from Running

In gym class we jog 6 minutes around the gym. Sometimes longer, depending on how much effort the coach feels we gave. For the rest of the day, my ankles and knees are sore. A kind of uniform throbbing akin to growing pains from elementary school.
Kinda annoying. Is this a result of me just being as unfit as I am, or something to do with my running style, shoes, etc.? I'm approx. 6 feet, if height plays a significant role in things.

I believe your weight would be more of a factor in this than your height, and it could just have to do with leg strength.

Weight's around 150-160 ish? Haven't measured in a long while, so that range might be low. I'm generally described as being really skinny though.

Do you run on the grass or in the gymnasium? Running on grass makes a world of difference in terms of impact on your legs.