Thomas Flint, 23, a carpenter, of Brantwood Gardens, Enfield, north London, will appear at Highbury Corner Magistrates Court on April 12, Scotland Yard said.
He is charged with throwing a missile on to the playing area, and using threatening, abusive or insulting words or behaviour or disorderly behaviour likely to cause harassment, alarm or distress.
Flint, who is understood to be an Arsenal fan, is on bail.
During the Premier League match at White Hart Lane, which Tottenham won 2-1, Tottenham's Wales international Gareth Bale had a banana thrown at him by Arsenal supporters.
Arsenal said on its website that if the individual charged was found guilty, he would also receive a stadium ban.