The 25-year-old was forced off the field for treatment during Wednesday's two-run victory over South Africa at Headingley, before returning to complete the match.
Stokes was deemed fit enough to play a big part in sealing a series win for England in Saturday's latest meeting, though, hitting a century in the second one-day international despite being in obvious discomfort at times.
It has now been confirmed that the Durham ace has had a scan to determine the full extent of the problem.
"It comes and goes. I have bad days and good days," he told BBC Sport. "I'm not sure if it is a worry or not, it might just be wear and tear. Hopefully we'll get a clearer picture.
"It's just the bowling. When I land on the floor I get a pain on the outside of my knee, so we just need to find out what that is.
"I was able to bowl today, but at the end of my third over I started to feel it. It's a confidence thing as well. If I feel the knee I don't feel I'm running through the crease properly."
England will hope to have Stokes available for their Champions Trophy opener against Bangladesh at The Oval next Thursday.