According to this
unless you have a knee injury/bad knees already running makes your knees stronger.
I'm no expert but I only really worry about things that only effect one side of my body, if both knees/claves/quads etc hurt I follow RICE Rest Ice Compression Elevation because it is normally an overuse injury. In the knee its prob an inflamed tendon but if it gets worse see a Physio (the doctor is going to give you anti inflammatory and send you to physio).
I pretty much always do stretch 5
https://www.self.com/gallery/best-stretches-for-knee-pain for my knees after a long run (I should before but don't) when doing this stretch you will hear a pop in the knee which releases the pressure and feels amazing. Foam roll as much as you can and do the full Foam roll guide
(I like this one for reasons

) when the glutes are tight it can effect the ankle that messes up the calf that messed up the knee.