Does the pain feel like someone jabbing you with a knife on the inside of the patella? I had this after starting running too many miles too fast when I started coaching cross country. It's called patella-femoral syndrome. As with most knee injuries it's caused by a muscle imbalance. The patella isn't tracking accurately through the groove in the distal end of the femur (thighbone). Your vastus medialis isn't strong enough. Do leg extensions by just sitting and holding your leg straight out for 30 seconds. Do 5 sets of these several times a day. Ice and ibuprofen may also help. Build your mileage slowly. Don't work through the pain, but stop as soon as any pain shows up. Just an armchair diagnosis. But if this is the problem, it will get better.