You don't tell us specifically what sort of problem you're having. The best advice given so far is to have an examination, and preferably by an ortho guy who is involved in sports medicine.
However....We reallize that such luxuries are not available to all....
Where does it hurt? The standard wisdom is that if you are having pain in the front of the knee, around the kneecap, then your are "hyperflexing" the knee. Your saddle is too low, or too far forward, or both.
If it is in the back of the knee, then you may be hyperextending. Your saddle is too high/too far back.
Pain on the sides of the knee often indicates a torn or otherwise damaged cartilage. That's what I had; required arthroscopic surgery.
If the pain is due to incipient arthritis, then the cartilage inside the knee, the cartilage that actually cushions the joint, may be wearing thin. Usually, in early stages, a cortisone shot will make everything pretty decent for some months.
Short of all that, try the old R.I.C.E. treatment. That's Rest, Ice, Compression, Elevation. Quit riding, ice the knee, keep it in an ace bandage or brace, and keep it elevated. Try this for at least several days, preferably a week.