The Firhill boss was sent to the stand by referee Stephen Finnie during the second half of Thistle's 1-0 Irn-Bru First Division loss after reacting to the whistler's decision to show midfielder Paul Paton a straight red card for a challenge on Accies' Stevie May.
McNamara will travel to Hampden to plead his case in a bid to avoid being handed a touchline ban that would force him to watch on from the stands in the coming weeks.
The New Douglas Park incident was the second time the Jags gaffer has been dismissed in his managerial career having also been sent-off during a First Division match at home to Raith Rovers last season.
It is not just McNamara who has seen red this season, with a several of his players sent off already this term.
Hugh Murray has received two red cards against Forfar and Morton while Paton, Steven Craig, for violent conduct against Cove Rangers, and Aaron Muirhead, for a last-man challenge during Saturday's Scottish Cup defeat to Dunfermline, have also been dismissed.
McNamara insists he is not worried by the Jags card count, however, and the Thistle manager hopes decisions will soon start to even themselves out.
He said: "If the players had a really bad disciplinary problem then we would be acting on it.
"Hugh got a straight red against Forfar, you could argue he was last man, the Morton game was two yellows.
"Paton was a straight red, which we didn't think it was at the time, but because he has left the ground it is hard to appeal it. The lad made the most of it and got up and played no problem.
"Saturday's was a last man and Steven Craig was just petulant, he reacted to the tackle against Cove, which is preventable.
"I think things have maybe went against us a bit, although most teams would maybe say that.
"We had Paton out for two weeks when he barely made contact with the lad, but you get a horrendous challenge on Stuart Bannigan that should have been a red card.
"Instead we have who is out for three weeks in Stuart. You hope, though, that these things even themselves out over the season.
"We have lost three games and the two in the league, at Hamilton and Morton, we have been down to 10 men but we have kept ourselves in the game."