If his knee hurts continuously without mechanism of injury time for an X-ray. If he had pain in other joints that resolved, he may have a post-viral synovitis, which will resolve over a few weeks. Children's Ibuprofen is safe for a 3 year old and may help.

If it gets boggy, swollen, or if he can't bend it, time to see the pediatrician. Juvenile RA is much less likely