- 2× Super Bowl champion (XLI, 50)
- Super Bowl MVP (XLI)
- 5× NFL Most Valuable Player (2003, 2004, 2008, 2009, 2013)
- 2× NFL Offensive Player of the Year (2004, 2013)
- NFL Comeback Player of the Year (2012)
- Walter Payton NFL Man of the Year (2005)
- 7× First-team All-Pro (2003–2005, 2008, 2009, 2012, 2013)
- 3× Second-team All-Pro (1999, 2000, 2006)
- 14× Pro Bowl (1999, 2000, 2002–2010, 2012–2014)
- 3× NFL passing yards leader (2000, 2003, 2013)
- 4× NFL passing touchdowns leader (2000, 2004, 2006, 2013)
- 3× NFL passer rating leader (2004–2006)
- 2× NFL completion percentage leader (2003, 2012)
- NFL 2000s All-Decade Team
- NFL 100th Anniversary All-Time Team
- Indianapolis Colts Ring of Honor
- Indianapolis Colts No. 18 retired
- Denver Broncos Ring of Fame
- Denver Broncos No. 18 honored
- Bart Starr Award (2015)
- 3× Bert Bell Award (2003, 2004, 2013)
- Sports IllustratedSportsman of the Year (2013)
- Maxwell Award (1997)
- Davey O'Brien Award (1997)
- Johnny Unitas Golden Arm Award (1997)
- Campbell Trophy (1997)
- Consensus All-American (1997)
- SEC Player of the Year (1997)
- First-team All-SEC (1997)
- Second-team All-SEC (1996)
- Tennessee Volunteers No. 16 retired
- NFL records
- Most passing touchdowns in a season: 55
- Most passing yards in a season: 5,477
- Most touchdown passes in a game: 7 (tied)
- All-time game-winning drives leader: 54
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