In the midst of a sterling rehab post-meniscus and ACL surgery, I developed a sharp, very localized pain at the side of the knee (first noticed in the rehab pool, strangely enough). It was something called the IT band. A couple of sessions of specific therapy (mostly the electrical-stimulation thing where they put the electrodes on your knee and you can turn up the wick as necessary) helped a lot.
I hope it's something as simple as this. As bad as the pain was, apparently it was not uncommon, probably due to certain rehab exercises putting an unusual strain on the knee. I did have to scale back stuff like treadmill speed and rehab weights for a few weeks, but the pain went away in time. Good luck.