The 26-year-old, who has played 40 times for his country, underwent surgery on Monday.
"Iain Henderson had surgery today to repair a torn ligament in his thumb. This is expected to make him unavailable for selection for approximately 10 weeks," Ulster said in a statement on their website.
That would rule Henderson out of Ireland's opening Six Nation test against England in Dublin on Feb. 2 as well as the matches against Scotland and Italy that follow as they bid to reclaim the title they won last year.
(Reporting by Ed Osmond, editing by Nick Mulvenney)