Baylor has won seven team national championships, all in the Big 12 era.
Matt Knoll and the 2004 Baylor men's tennis team claimed the school's first-ever NCAA team championship when they defeated UCLA 4-0 at the NCAA Championships in Tulsa, Okla. The Bears posted a program-best 32-2 record and ended the season ranked No. 1 in the Intercollegiate Tennis Association's (ITA) national rankings.
Less than one year later, Kim Mulkey and the Lady Bear basketball team followed suit with a dominating 84-62 victory over Michigan State in the NCAA championship game to secure the first women's team national title in school history. The Lady Bears posted a 33-3 record, the best mark in school history, 14-2 in Big 12 Conference play and a perfect 14-0 at home en route the NCAA Championship and the Big 12 regular season and tournament titles. The Lady Bears also finished the season with a school-record 20-game winning streak, and as the No. 2 seed in the Tempe Regional, became only the fourth men's or women's basketball team to win the title by knocking off three straight No. 1 seeds - North Carolina, LSU and Michigan State.
Coach Ellen White and the Baylor equestrian's Hunter Seat team took home its first national championship in 2012 with a thrilling victory over Texas A&M that came down to a 1192-1070 win on points after a 4-4 tie at the National Collegiate Equestrian Association Championship at Extraco Events Center in Waco. The victory also ensured a third place finish overall, the highest finish in program history.
Coach Mulkey and the Lady Bears captured their second national title in 2012, capping off a perfect 40-0 season with a dominating 80-61 victory over Notre Dame in the NCAA women's basketball championship game. They became the seventh women's team to run through a season unbeaten and the first in NCAA history to win 40 games.
Coach Felicia Mulkey and the Baylor Acrobatics & Tumbling team claimed the program's first-ever NCATA Championship in 2015, defeating Oregon, 286.690-282.870, at Fairmont State's Joe Retton Arena in Fairmont, W.Va. The Bears won five of the six events to claim the national crown. BU claimed victories in compulsory (39.05-39.95), acro (29.50-28.25), pyramid (29.75-29.60), toss (29.20-29.15) and the team event (101.69-98.97).
Coach Mulkey and A&T repeated in 2016, dominating No. 2 seed Oregon from the opening compulsory heat and capturing their second consecutive NCATA National Championship before a record Ferrell Center crowd of 2,163. The Bears won all six events and outscored the Ducks, 286.275-282.305.
In 2017, the second-seeded Bears dominated the team event to win their third consecutive NCATA national championship by beating top-seeded Oregon (279.350-275.625) in a nip-and-tuck final at the Felix Event Center in Azusa, Calif.
Aside from the seven national titles, Baylor has won 41 NCAA individual championships. Appropriately branded "Quartermile U", Baylor has won 20 national titles in the 4x400 meter relay.
A complete list of Baylor's national championships are listed below:
 |
Team National Championships |
| Year | Sport | Team | Head Coach |
| 2017 | Acrobatics & Tumbling | 2017 NCATA National Champions | Felicia Mulkey |
| 2016 | Acrobatics & Tumbling | 2016 NCATA National Champions | Felicia Mulkey |
| 2015 | Acrobatics & Tumbling | 2015 NCATA National Champions | Felicia Mulkey |
| 2012 | Women's Basketball | 2012 Women's Basketball National Champions | Kim Mulkey |
| 2012 | Equestrian | 2012 NCEA Hunter Seat National Champions | Ellen White |
| 2005 | Women's Basketball | 2005 Women's Basketball National Champions | Kim Mulkey |
| 2004 | Men's Tennis | 2004 Men's Tennis National Champions | Matt Knoll |
|
Individual National Championships |
| Year | Sport | Name(s) | Event |
| 2014 | Men's Track & Field (Outdoor) | Trayvon Bromell | 100m |
| 2014 | Men's Track & Field (Outdoor) | Felix Obi | Triple Jump |
| 2009 | Men's Track & Field (Indoor) | Trey Harts | 200m |
| 2009 | Men's Track & Field (Indoor) | LeJerald Betters, Marcus Boyd, Trey Harts, Quentin Iglehart-Summers | 4x400 |
| 2008 | Men's Track & Field (Outdoor) | LeJerald Betters, Marcus Boyd, Justin Boyd, Quentin Iglehart-Summers | 4x400 |
| 2008 | Men's Track & Field (Indoor) | LeJerald Betters, Marcus Boyd, Justin Boyd, Trey Harts | 4x400 |
| 2007 | Men's Track & Field (Outdoor) | LeJerald Betters, Quentin Iglehart-Summers, Kevin Mutai, Reggie Witherspoon | 4x400 |
| 2007 | Men's Track & Field (Indoor) | LeJerald Betters, Quentin Iglehart-Summers, Kevin Mutai, Reggie Witherspoon | 4x400 |
| 2006 | Men's Track & Field (Indoor) | Jacob Norman | 60m |
| 2005 | Men's Track & Field (Outdoor) | Darold Williamson | 400m |
| 2005 | Women's Tennis | Zuzana Zemenova |
Singles |
| 2005 | Men's Tennis | Benjamin Becker |
Singles |
| 2004 | Men's Track & Field (Outdoor) | Braelon Davis, Wil Fitts, Jeremy Wariner, Darold Williamson | 4x400 |
| 2004 | Men's Track & Field (Outdoor) | Jeremy Wariner | 400m |
| 2004 | Men's Tennis | Benedikt Dorsch | Singles |
| 2004 | Men's Track & Field (Indoor) | Jamen Saziru, Mark Teter, Jeremy Wariner, Darold Williamson | 4x400 |
| 2004 | Men's Track & Field (Indoor) | Jeremy Wariner | 400m |
| 2002 | Men's Track & Field (Indoor) | Michael Smith, Charles Sterling, Zsolt Szeglet, Darold Williamson | 4x400 |
| 2001 | Men's Track & Field (Outdoor) | Brandon Couts, Bayano Kamani, Zsolt Szeglet, Floyd Thompson | 4x400 |
| 2001 | Men's Track & Field (Outdoor) | Bayano Kamani | 400m Hurdles |
| 2000 | Men's Track & Field (Outdoor) | Brandon Couts, Bayano Kamani, Zsolt Szeglet, Floyd Thompson | 4x400 |
| 2000 | Men's Track & Field (Indoor) | Brandon Couts | 400m |
| 1999 | Men's Track & Field (Outdoor) | Bayano Kamani | 400m Hurdles |
| 1999 | Women's Track & Field (Outdoor) | Stacey Bowers | Triple Jump |
| 1998 | Women's Track & Field (Indoor) | Angelique Banket, Alayah Cooper, Jennifer Jordan, Yulanda Nelson | 4x400 |
| 1998 | Men's Track & Field (Indoor) | Stephan Bragner, Brandon Couts, Damian Davis, Mario Watts | 4x400 |
| 1996 | Men's Track & Field (Outdoor) | Michael Ford, Raoul Howard, Marlon Ramsey, Darrin Strong | 4x400 |
| 1995 | Men's Track & Field (Outdoor) | Michael Ford, Raoul Howard, Darrin Strong, Corey Williams |
4x400 |
| 1995 | Men's Track & Field (Indoor) | Deon Minor | 400m |
| 1992 | Men's Track & Field (Indoor) | Daniel Fredericks, Ethridge Green, Deon Minor, Corey Williams | 4x400 |
| 1992 | Men's Track & Field (Indoor) | Deon Minior | 400m |
| 1991 | Men's Track & Field (Outdoor) | Lester Crenshaw, Ethridge Green, Daniel Fredericks, Corey Williams | 4x400 |
| 1991 | Men's Track & Field (Indoor) | Ethridge Green, Daniel Fredericks, Tony Miller, Corey Williams | 4x400 |
| 1990 | Men's Track & Field (Outdoor) | Daniel Fredericks, Michael Johnson, Tony Miller, Todd Thompson | 4x400 |
| 1990 | Men's Track & Field (Outdoor) | Michael Johnson | 200m |
| 1990 | Men's Track & Field (Indoor) | Ethridge Green, Michael Johnson, Tony Miller, Todd Thompson | 4x400 |
| 1990 | Men's Track & Field (Indoor) | Michael Johnson | 200m |
| 1989 | Men's Track & Field (Outdoor) | Raymond Pierre | 400m |
| 1989 | Men's Track & Field (Indoor) | Michael Johnson | 200m |
| 1985 | Men's Track & Field (Outdoor) | Willie Caldwell, Darnell Chase, Derwin Graham, Johnny Thomas | 4x400 |
| 1985 | Men's Track & Field (Indoor) | Willie Caldwell | 500m |
