Pedaling should be easy. Shift to a lower gear. If you have gotten used to putting a lot of muscle into pedaling, then you might be blowing your knees to all to heck.
Once your knees get to feeling better, get your seat back down to where is should be. To guess at a place to start, sit on your saddle as best you can and put the heel of your shoe (with your foot in the shoe) on the pedal and put it in the furthest locataion from you. If you don't have a very slight bend at your kneee then lower or raise your saddle till you do.
Go for a ride. It will feel stupid, but stay in a gear that is low (easy) enough to pedal with no effort what so ever. If you ever feel like you are using any leg muscle, then shift to an easier gear. After you've ridden for a time, how do your knees feel?
If they don't bother you, then keep using the easy gears to pedal in till it doesn't feel stupid anymore. After that you can graduate to using a little muscle and harder gears briefly as you accelerate rapidly.
Whether your knees actually have some issue that need a medical professional to look at is on you. So consider if you need to go to one.
Last edited by Iride01; 09-17-20 at 04:53 PM.