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.