Gary Whybrow, 31, Sam Parsons, 24, and Peter Ditchman, 52, are accused of using threatening, abusive or insulting words and are due to appear at Hendon Magistrates' Court on February 4.
Many Spurs fans, both Jewish and non-Jewish, call themselves the "Yid army" and Spurs players as "Yiddos".
The Football Association issued new guidelines last year and suggested any supporters using the term could face criminal action.
Whybrow and Parsons are accused of the offence during the Europa League game against FC Sheriff on November 7, while the third fan is alleged to have used bad language in the Premier League clash with West Ham on October 6.
The three men are all accused of using threatening, abusive or insulting words or behaviour or disorderly behaviour within the hearing or sight of a person likely to be caused harassment, alarm or distress.
Police have repeatedly warned fans not to use the word "yid" in recent months, and have also made arrests over various anti-Semitic tweets aimed at Spurs fans.
Chants using the 'Y-word' has been a controversial subject in north London for some time.
A Tottenham Supporters Trust statement read: "It remains our firm belief that, when used in a footballing context by Tottenham Hotspur supporters, there is no intent or desire to offend any member of the Jewish Community."