Flannery, who returned to training earlier this month, has been troubled by a calf injury. His last appearance for Munster was as a replacement in their bonus point victory over Toulon in the Heineken Cup in October.
The Munster team and replacements will be announced on Friday afternoon.
Meanwhile, the province's Magners League win over Connacht came at a price when forwards Alan Quinlan and Dave Ryan were forced to retire with injuries. They now face several weeks on the sidelines.
Quinlan, Munster's most-capped player, dislocated his elbow during the second half of the match at the Sportsground. It was put back in place at hospital afterwards.
He met with a specialist yesterday and is expected to be out of action until mid to late February.
Promising prop Ryan, who was injured in the dying minutes of the game, has not been named in the squad for the Ulster game after a scan revealed an acute shoulder injury.
He will now see a specialist next week and is expected to be out for several weeks, and may undergo surgery.
Quinlan's back row colleague James Coughlan, who was not involved against Connacht, has a suspected cheekbone injury and is due to see a specialist today.
MUNSTER Squad (v Ulster) - Backs (12): Tomas O'Leary, Peter Stringer, Conor Murray, Scott Deasy, Paul Warwick, Barry Murphy, Tom Gleeson, Sam Tuitupou, Keith Earls, Lifeimi Mafi, Denis Hurley, Doug Howlett.
Forwards (16): Wian du Preez, Darragh Hurley, Tony Buckley, John Hayes, Peter Borlase, Jerry Flannery, Mike Sherry, Damien Varley, Billy Holland, Mick O'Driscoll, Ian Nagle, Donnacha Ryan, Niall Ronan, Paddy Butler, Tommy O'Donnell, Denis Leamy.