There are a couple of common causes of knee pain in runners.
The first is called patellofemoral pain syndrome (runner's knee). This is basically a degeneration of the cartilage in the knee cap (patella) due to misalignment of the knee cap with repetitive motion. The pain is usually under the knee cap or on the inside edge. Treatment for patellofemoral pain syndrome involves cutting back on high impact exercise, stretching exercises to loosen the calf and hamstring muscles, and straight leg raises (avoid anything that puts pressure on a bent knee). Shoes to correct pronation may also be needed.
The second is called iliotibial band syndrome. This is an overuse injury
of the band of tissue running down the outside edge of the thigh and knee. The pain is usually on the outside edge of the knee cap. In addition to cutting down on running, especially running on inclines, stretching exercises to loosen the iliotibial band are important (you can talk to your personal trainer or gym coach to help you with these exercises).
I recommend talking to your primary care doctor
or a sports medicine doctor
to obtain a definitive diagnosis and for more help deciding how best to treat the problem.