Hearts secured their passage to the final of the Scottish Cup against city rivals Hibernian, following a controversial late penalty by former Celt Craig Beattie.
Lennon was handed a two match ban last over a separate incident, has been charged with misconduct relating to offences which include aggressive behaviour and insulting language towards the match official.
The Northern Irishman ran on to the pitch to confront referee Euan Norris at full-time, over the decision to award a penalty to Hearts in the closing stages of the game. Lennon has also been hit with two charges relating to comments posted on his personal twitter page soon after the game ended.
Lennon said he thought that the referee’s decision was “personal”, and then re-tweeted a comment from a Celtic fan which suggested the club “get out of this league that is run by crooked SFA officials”.
If found guilty of these latest charges, Lennon will watch Celtic’s start to next season’s defence of the SPL title from the stand.