There's a lot to be said for (1) fit, including cleat wedges and orthodics, if necessary, (2) warming up and cooling down, (3) ramping up your endurance to longer rides and (4) not over stressing your body, whether that means proper rest between rides or spinning in a higher cadence up hills. It's difficult to say what the issue is without knowing more about your current fit, the pain you are experiencing (not just the location) and any prior symptoms.

I endured knee pain that sounds similar, but may or may not have been what you are going through, and after going to the dr, it was cleared up through a regimen of NSAIDs and a professional fitting.