He was taken straight to hospital after being stretchered off the pitch in the 45th minute.
"He landed on his head and was knocked out, so the medical team checked there was no neck damage," said Dave Jones.
"He has 'pins and needles' in his hands but he had all the checks in hospital and he's fine, so that's a good sign."
It's unknown how long he'll be out of the side.
McNaughton had only been on the pitch for a couple of minutes when he was injured. He'd come on as a replacement in the 42nd minute for Joe Ledley who picked up a knee injury. It's unknown exactly how serious that is.
The knocks received mean both players miss their international call ups this coming week. They join Darren Purse and Riccy Scimeca on the treatment table.