Google "PFPS" otherwise known as runners knee. Pretty much is a dull pain caused by the mis-tracking of your patella tendon over the kneecap. There are multiple causes for this which include, muscle imbalances between quads/hams, weak hips, imporper running shoes/form, too much-too soon.
Treat the all muscles of the leg to recover, you'd be amazed how much all the leg muscles work together and something like a tight calf could have an impact to the muscles in your upper leg. See what the doc says, but it's pretty much a guarantee he will give the textbook "rest, ice and stay off it for a couple weeks" A sports doctor would be your best bet if it doesnt improve.
Also I tend to do single leg exercises for strengthing. Single-leg deadlifts, single-leg squats, wall-sits.