@cookiezz, I'm dealing with a Baker's cyst on my left knee right now too. Luckily physical therapy and doing my daily exercises diligently is helping. but s l o w l y.

I find that improvement came in very teeny tiny steps at first and accompanies by some setbacks. Icing and rest helps most during the setbacks. The exercises I was given didn't only focus on the knee but also my ankle, my hip and lower back. These areas also needed strengthening or management because they were compensating for poor posture due to the pain in my knee. It's all connected, right?

Now after about 8 weeks, I'm feeling a lot better. Not completely healed, but I see significant improvement and can do the things I like to do again. I'm going on a hiking trip in June so that'll be the real test.

I think you're wise to see your doctor to make sure it isn't something else going on and to rule out a meniscus tear or other injury. If Baker's cyst is confirmed, then maybe a check in with the physical therapist to make sure you're doing the exercises correctly and not over doing it.