Lennon has been accused of breaking the terms of his three-match suspension by being in the "playing zone" within 15 minutes of the final whistle of Celtic's 3-1 defeat by Motherwell on Sunday.
He will now face an SFA hearing on 23 May - three days before Celtic face Hibernian in the Scottish Cup final, raising the prospect of him being confined to the Hampden stands.
The former Celtic skipper revealed he had been summoned to the Fir Park match officials' room by referee Euan Norris after the second match of his three-game ban.
Lennon told Sky Sports on Sunday: "He (Norris) called me into his room. It was about a number of things but we'll leave that confidential for now."
The Celtic boss had seen a suspended three-match ban triggered by an SFA charge for using offensive language towards St Mirren captain Jim Goodwin.
Kilmarnock boss Kenny Shiels also found himself in trouble on Friday, incurring an SFA notice of complaint.
Shiels, who has been involved in a public row with Lennon over the PFA Scotland player of the year shortlist, has been accused of breaking two rules over comments he made in a media interview this week.
Lennon had compared Shiels to comic character David Brent following the Kilmarnock manager's withering reaction to his counterpart's criticism of the lack of Celtic players on the awards shortlist.
But Shiels landed in hot water after telling BBC Radio Scotland: "(Celtic) have got a massive influence in the judicial panel and things like that, decisions that's made. Celtic are the monster of Scottish football."
The Killlie manager has been accused of both bringing the game into disrepute and not acting in the best interests of football by making comments that "call into question the impartiality of the Judicial Panel and the integrity of another member club of the Scottish FA".
Kilmarnock have, in addition, effectively been charged with failing to control their manager.
The Rugby park club have been accused of breaking rule 2, by "failing to procure that one of your team officials, namely Kenny Shiels, Manager, acts in accordance with Disciplinary Rule 1 and complies with the Judicial Panel Protocol)."