The 26-year-old Scot missed the midweek defeat to Leicester and was instead expected to be recuperating following an operation to repair cartilage damage.
"He's going for an operation on Wednesday with a cartilage tear," said boss Danny Wilson after Tuesday night's defeat.
"We've been dealt some rough cards but we've got to get on with it."
O'Brien has been a regular starter for the Reds this season, making 30 appearances and scoring three goals.
He is in his fourth season at Oakwell after joining the club for an undisclosed fee from Motherwell in June 2010 and signed a new two-year contract with the Reds in the summer of 2012.