Best is suffering from an underlying, chronic disc injury on his neck which requires surgery and a lengthy recovery period of between nine and 12 months.
The extent of the problem was discovered after the 26-year-old complained of pain in the neck area recently and subsequently underwent further medical investigation to assess the extent of any problem.
The absence of one of their most respected and influential players so close to the start of the new campaign is clearly a massive setback for Ulster, who start the season with new coach Brian McLaughlin at the helm.
"Obviously losing Rory at the start of the season is a huge blow for us," said Ulster's operations director and former Ireland fly-half David Humphreys.
"Not only is he our No1 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."