Wycombe goalkeeper Jordan Archer was attacked by a fan in the closing stages of the visitors' 1-0 win at the Priestfield Stadium.
Kent Police confirmed a man has been arrested on suspicion of assault following the incident.
The supporter jumped on top of the 19-year-old, who is on loan from Tottenham, in injury time.
The player did not receive treatment, was not hurt and carried on for the remaining few seconds of the match.
Archer had just been booked for time-wasting but was unhurt in the incident.
"There are silly people sometimes at football grounds," said Wycombe manager Gareth Ainsworth.
"They give the rest of the Gillingham fans a bad name.
"I know Jordan, he's a tough lad. I don't want to comment on it too much but everyone's OK."
In October, Leeds fan Aaron Cawley was jailed for 16 weeks for attacking Sheffield Wednesday goalkeeper Chris Kirkland.