Something in your knee could be rubbing wrong, not very techincal, I know. Could be do to a lack of cushion or inflamation.
Even if it doesn't hurt all the time I would still R.I.C.E and plan on taking more rest days in between run days, and stretch, a lot, foam rolling could be good as well, I just ordered this thing called The Stick, it's the same concept as a foam roller but easier to use and store.
If it doesn't stop you might want to get it looked at, continuing knee pain isn't something you want to develop into a bigger problem.
Also, taking a supplement with msm, glucosamine and chondroitin wouldn't hurt and might help if it's an issue with fluid/connective tissue/joint lubrication
Good luck!
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