The D3football.com All-Decade team of the 2000s encompasses the years 2000-2009. To be eligible, a player had to finish in that span or play the majority of his career then, three seasons.

Any player who met those criteria was considered on the basis of his full career, whether he started playing in 1997, such as R.J. Bowers of Grove City, or finished in 2010, such as Cecil Shorts of Mount Union.

Pos. First team QB Greg Micheli, Mount Union RB Nate Kmic, Mount Union RB Justin Beaver, UW-Whitewater WR Pierre Garcon, Norwich-Mount Union WR Blake Elliott, St. John's TE Michael Allan, Whitworth T J.D. Sheldon, Augustana G Derek Blanchard, Mount Union C Josh Knox, Hardin-Simmons G Josh Warner, Brockport State T Blaine Westemeyer, Augustana Defense DE Bryan Robinson, Wesley DT Adam Haas, Cortland State DT Ryan Kleppe, UW-Whitewater DE Jeremy Hood, St. John's LB Jerimiah Janssen, St. Norbert LB Jerrell Freeman, Mary Hardin-Baylor LB Jermaine Taylor, Bridgewater (Va.) CB Pete Ittersagen, Wheaton (Ill.) S Kyle Hausler, Capital S Josh Kubiak, Mary Hardin-Baylor CB Clinton Tabb, Rowan Special teams RET Larry Beavers, Wesley K Jeff Schebler, UW-Whitewater P Alex Groh, Occidental     Pos. Second team QB Brett Elliott, Linfield RB R.J. Bowers, Grove City RB Chuck Moore, Mount Union WR Nate Jackson, Menlo WR Cecil Shorts, Mount Union TE Jeff Gibbs, Otterbein T Brennan Fortune, St. John Fisher G Mackenzie Hay, Augustana C Eric Safran, Mount Union G Adam Hernandez, Hardin-Simmons T Jason Lewis, Mount Union Defense DE Andy Studebaker, Wheaton (Ill.) DT Gerard Bryant, St. Lawrence DT Brandon Tisdale, Wilmington DE Steven Wilson, King's LB Adrian Pynenberg, Wabash LB Ron Swearingen, Capital LB Kyle Follweiler, Wilkes CB Tony Beckham, UW-Stout S Matt Kostelnik, Mount Union S Derrick Williams, Mary Hardin-Baylor CB Chris Kern, Mount Union Special teams RET Pete Ittersagen, Wheaton (Ill.) K Carlos Martinez, Buena Vista P Kevin Soflkiancs, Baldwin-Wallace     Pos. Third team QB Tom Arth, John Carroll RB Mark Robinson, St. John Fisher RB Tony Sutton, Wooster WR Casey Allen, Linfield WR Michael Coleman, Widener TE Jon Lanouette, Wesley T Max Sakellaris, UW-Whitewater G Alex Bell, Hobart C Josh Ostrue, St. Thomas G Adam Grossman, Ithaca T Jeff Oliver, Mary Hardin-Baylor Defense DE Jason Trusnik, Ohio Northern DT Vince King, Wartburg DT Matt Williamson, Mount Union DE Jarrell Chandler, Salisbury LB A.J. Raebel, UW-Whitewater LB Preston Meyer, Mary Hardin-Baylor LB Gene Lang, St. John Fisher CB Alex Hansen, Hardin-Simmons S Rocky Myers, Wesley S Frank Pilato, Washington and Jefferson CB Steve Stepnick, St. John Fisher Special teams RET Blake Elliott, St. John's K Mike Clark, Augustana P Scott Verhalen, East Texas Baptist     Pos. Fourth team QB Chad Johnson, Pacific Lutheran RB Tom Arcidiacono, Union RB Phil Porta, Bethel WR Jack Phelan, Hartwick WR Jerheme Urban, Trinity (Texas) TE Jon Branche, RPI T Ben Knepper, UW-Stout G Jon Stavast, Luther C Thomas Anderson, Hardin-Simmons G Brandon Bennett, Willamette T Larry Kinnard, Mount Union Defense DE Matt Campbell, Mount Union DT Pat Ryan, Benedictine DT Nick Gunderson, St. John's DE Marcus Ball, UW-Stout LB Matt O'Bryant, Millsaps LB Cam McCambridge, St. John's LB Beau LaBore, St. John's CB Will Galusha, Hardin-Simmons S Aaron Lewis, Carnegie Mellon S Brandon Carr, Bethel CB Byron Westbrook, Salisbury Special teams RET Joshua Carter, Muhlenberg K Scott Birkhofer, Linfield P Cory Ohnesorge, Occidental

Blaine Westemeyer Clinton Tabb R.J. Bowers Matt Kostelnik Michael Coleman Alex Hansen Byron Westbrook