A Grand Slam winner last season and captain for Ireland's recent successful summer tour, the 26-year-old hooker had been named in the Irish squad for the upcoming training camp in Limerick, which begins on Sunday.
Best played in all ten of Ireland's Test matches last season, ending the campaign on a high with his fourth international try in June's 27-10 victory over the USA.
The shock news comes as a serious setback for new Ulster coach Brian McLaughlin, with the start of the new Magners League season just over three weeks away.
Ulster's Operations Director David Humphreys commented: "Obviously losing Rory at the start of the season is a huge blow for us, not only is he our number 1 hooker but also our captain and one of the most experienced players in the squad.
"However, what is most important is Rory's long term health and welfare and there's no reason not to expect him to return fully to rugby, post surgery and rehabilitation, next season.
"The timing of this injury presents difficulties as most players are contracted for the 2009/10 season.
"While we strengthened our hooking options this summer with the signing of Andy Kyriacou, we are working at present to find a replacement for Rory within world rugby."
Best, who was recently married, intends to take some holiday time prior to surgery to come to terms with his injury. The date for the operation has not yet been set.