in my experience (providing its not something more serious) it could be one, or a combination of the following causing an imbalance - Tight Hamstrings, weak or tight calves, weak gluteus medius.
Pain on the inside of the knee is a common symptom of patella femoral syndrome, or as they called it in my day 'chondromalacia patella.' I suffered from this way back in '84 and the treatment was to strengthen the vastus medialis muscle (inner thigh) in isolation with short range leg extensions using a loose weight strapped to the ankle. This worked very well for me and I still do them to this day. The idea is that you put a weight in each of a pair of socks,(eg: tin of beans) tie them together and hang them over your ankle. Sit on the edge of a bed or settee and straighten your leg out to full extension whilst pointing your toes up hard towards your face. It's just the last few degrees of angle that isolate the vastus medialis, hence the socks so you're not taking up the load too early. Also, ice after running and I used ibuprofen gel in the early days until it all cleared up.
However, I would run this message past your physio first before trying as treatments and ideas change over the years. All I know is that I'm still here, still running after all these years with no knee pain.
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