Before the beginning of his 2006 senior season, there was speculation that Leak might not be the Gators' starting quarterback due to the emergence of talented freshman Tim Tebow.[SUP][4][/SUP] Instead, Meyer publicly endorsed Leak as the starting quarterback and confirmed Tim Tebow would be the back-up. Preseason analysis projected that Florida would have the hardest schedule in the country, including back-to-back games against Tennessee, Kentucky, Alabama, LSU, Auburn and Georgia. The 2006 season proved to be a redemption year for Leak: leading the Gators to their first SEC Championship since 2000, and a spot in the 2007 BCS National Championship Game against Ohio State University (the Gators' first championship game appearance since 1996). Leak also broke many Gators' passing records set by Heisman Trophy-winner Danny Wuerffel, including Wuerffel's record for career passing yards set during the 2006 SEC championship game.
Leak led the Florida Gators to their second consensus national championship with a 41–14 victory over the Ohio State Buckeyes on January 8, 2007, taking home the offensive Most Valuable Player (MVP) award for the game. His performance was solid throughout the BCS championship game, completing his first nine passes at the start of the game, and finishing with twenty-five completions in thirty-six attempts for 213 yards and one touchdown.