Greene played quarterback at the University of Georgia in college. He began his career as a redshirt freshman in 2001, being named the starter before the season. His most notable freshman game occurred at #5 Tennessee on October 6, known as the “Hobnail Boot” game. This phrase was coined by Georgia’s famous play-by-play announcer Larry Munson. After Tennessee took the lead in the fourth quarter on a successful screen pass with :44 left, Greene led the Bulldogs back down the field with an inspiring series of quick passes. The winning touchdown pass went to fullback Verron Haynes in a now famous play known as “P-44 Haynes” or the “Hobnail Boot” play with just five seconds remaining on the clock. Upon Greene’s completion to Haynes in the endzone for the winning touchdown, announcer Munson made this fateful call: “We just stepped on their face with a hobnail boot and broke their nose. We just crushed their face!”

This play marked the beginning of Greene’s record-setting career at Georgia, highlighted by guiding the team to a Sugar Bowl victory in 2002. The same season he led the Bulldogs to their first SEC championship since 1982. He was named SEC Offensive Rookie of the Year after the 2001 season, and was the 2002 Offensive Player of the Year for The Southeastern Conference. In 2004, Greene made 214 consecutive pass attempts without an interception, a record that stood until broken by Andre Woodson from Kentucky in 2007.

Greene finished his college career as the winningest quarterback in NCAA Division I history with 42 wins in four years, eclipsing the record previously held by Peyton Manning. However, on November 21, 2009, University of Texas quarterback Colt McCoy broke his record with a win over University of Kansas. Greene finished his college career as the Southeastern Conference all-time career leader in yards gained with 11,270 until that record was broken by Aaron Murray on October 5, 2013, against Tennessee.