Simplex

Seconding advice to raise the saddle, when it is too low your legs are unable to fully extend on every down-stroke and on the upstroke the angle-bend is too high; over time this can cause chronic inflammation in the knee joint.

I used to have pain in my outer knee on my left side, probably due to over-training and taking on too much mileage too quickly. After a bike fit it was determined that I have dominance on my right which was further proven by some embarrassing balancing exercises. In order to right this imbalance I was given single-pedal exercises to perform with each leg separately. So you find a quiet road, put your bike into a very easy gear, unclip one foot and pedal with the other side slowly while trying to maintain balance and a consistent circular pedal stroke for say a couple minutes, repeat for the other side.

At my fit my saddle was also raised by about 5mm. The fitter told me that the likely reason I was getting the pain on one side was because of cycling on a saddle that was too low for a long period of time (for me it was about a year and a half). I backed off my training for a month (partly due to a crash, which did not help) and took things very easily and since then I have been on a couple tours and have not seen the pain come back.

I think it is essential to remember that even if you get the correct fit, the inflammation in the knees will likely still be present and can only disappear with rest; which unfortunately means not cycling for a couple weeks, or maybe very low intensity cycling for short periods. The irony is that cycling is meant to be good for your knees, and many sport physios will recommend it for people with chronic knee pain, I guess that is thrown out the window if you're blasting high gears up hills!