After two years of coming close, 2009 marked the breakthrough season for Stanford as it captured the fourth NCAA title in program history and first for men's gymnastics since 1995. The Cardinal scored 362.800 points to win the national championship in Minneapolis, Minn., by 1.3, while giving coach Thom Glielmi his first title. Stanford recorded team season-bests on still rings and parallel bars, and won two individual event titles to help boost itself atop the pack. In addition to the team title, seven athletes earned All-America honors in 11 events. The Cardinal was led by senior Sho Nakamori, who earned All-America honors on the parallel bars, horizontal bar and in the floor exercise. Also, earning multiple honors were Tim Gentry in the still rings and the vault and Nicholas Noone on still rings and parallel bars. In addition, Alex Buscaglia (horizontal bar), Bryant Hadden (still rings), Ryan Lieberman (parallel bars) and Kyle Oi (still rings) each earned All-America status.

The Cardinal captured its third NCAA title in four seasons by holding off Nebraska and Penn State in the finals in Columbus, Ohio, scoring 232.400 points to 227.325 for the Cornhuskers and 229.775 for the Nittany Lions. Sadao Hamada earned National Coach of the Year honors for the third time. Stanford was led by Ian Bachrach who captured the NCAA individual title on vault and had Stanford's top score during the team championships in the floor exercise. Keith Wiley (floor exercise and vault), Andrew Manson (rings), Jaime Ellis (parallel bars) and Tim Dalrymple (parallel bars) were among the other top Cardinal finishers.

Stanford repeated as NCAA champion to become the 11th team in history to earn back-to-back titles in men's gymnastics. The Cardinal held off runner-up Nebraska and third-place finisher, Ohio State, to take the title in Albuquerque, N.M. Head coach Sadao Hamada earned National Coach of the Year honors for the second consecutive season while Jair Lynch won the individual title on the parallel bars, the event in which he would win an Olympic silver medal in 1996.

Stanford earned its first NCAA title in men's gymnastics, behind National Coach of the Year Sadao Yamada. Stanford scored 289.575 points to edge hometown runner-up Nebraska by 0.625 for the title in Lincoln, Neb. Jair Lynch won the horizontal bar championship to become the first gymnast in school history to win that event.