I had this problem about a month ago and I paid to get professionally fitted. He moved my shoe away from the crank (a small amount). If you are going to do this, make very slight adjustments. My first (of two) fits, the guy put a wedge in both of my shoes, I believe that helped a lot. He said that is suppose to help with medial knee pain. In my opinion, a professional fit is well worth the cash if you are having a lot of knee pain.
But if you have been fitted and changed something...
I recently got new pedals, and I apparently positioned the cleat differently than the original ones. I didn't think it was going to make much difference. After about 1/2 hour on the bike, my left knee developed a burning sensation under the kneecap. I moved the cleat forward (e.g. moved my foot rearward) back to where I'm pretty sure it was before. Viola, no more knee pain.
Long story short - if you made a change try to get back to the position you were before. Also - cleat position definitely makes a difference in the knees.
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