Originally Posted by RNAV

Definitely get a professional fit if you're going to be doing anything other than casual riding. Just make sure you're going to a reputable fitter. Like you, I had left knee pain. Spent probably $1,000 going to different fitters, never could get the pain to go away. Then I measured my sit bones and discovered I have exceptionally narrow sit bones (100mm). Rule of thumb is that your saddle should be ~20mm to 30mm wider than your sit bones. First fitter measured me, didn't have a narrow enough saddle (didn't tell me this), so put me on the narrowest saddle he had (138mm). All other fitters kept me in the same saddle. On a whim, I decided to try a Berk Lupina saddle. It's 132mm, but has a really round shape and feels narrower than it is. Knee pain went away immediately, and hasn't come back since.

Long story short: your saddle could be too wide (in addition to being too high, too set back, improper cleat position, etc.).