The 19-year-old - on loan from Tottenham - was placing the ball prior to taking a goal kick when the supporter entered the field and leapt towards him at the Priestfield Stadium on Monday night.
The fan was quickly apprehended by a steward and led away.
Wycombe boss Gareth Ainsworth told Sky Sports: "Some people give the rest of the Gillingham fans a bad name.
"I don't want to comment too much, but everyone is okay in there."
Gills boss Martin Allen was quick to condemn the incident. He said: "As a football club we can't condone (what happened). None of us are happy with that."