|1999 NCAA Division II football season|
|Regular season||August 28 – November 13, 1999|
|Playoffs||November 20 – December 11, 1999|
|National Championship||Braly Municipal Stadium|
|Champion||Northwest Missouri State (2nd title)|
|Harlon Hill Trophy||Corte McGuffey, Northern Colorado|
The 1999 NCAA Division II football season, part of college football in the United States organized by the National Collegiate Athletic Association at the Division II level, began on August 28, 1999, and concluded with the NCAA Division II Football Championship on December 11, 1999, at Braly Municipal Stadium in Florence, Alabama, hosted by the University of North Alabama.
Conference changes and new programs
- The Midwest Intercollegiate Football Conference transferred its football sponsorship, and 13 of its 14 members, back to the Great Lakes Intercollegiate Athletic Conference after the two leagues merged prior the season. The MIFC was then dissolved and GLIAC resumed its football championship for the first since 1990.
|School||1998 Conference||1999 Conference|
|Alabama A&M||D-II Independent||SWAC (I-AA)|
|Elon||D-II Independent||I-AA Independent|
|Grand Valley State||MIFC||GLIAC|
|Saginaw Valley State||MIFC||GLIAC|
|St. Francis (IL)||MIFC (D-II)||MSFA (NAIA)|
|Stony Brook||Eastern (D-II)||Northeast|
- After Mankato State University changed its name to Minnesota State University, Mankato in 1999, the Mankato State Mavericks became the Minnesota State–Mankato Mavericks.
Central Intercollegiate Athletic Association – Winston-Salem State
|1999 NCAA Division II Football Championship|
The 1999 NCAA Division II Football Championship playoffs were the 26th single-elimination tournament to determine the national champion of men's NCAA Division II college football. The championship game was held at Braly Municipal Stadium in Florence, Alabama, for the 13th time.
Braly Municipal Stadium
|Fort Valley State||17|
|Northwest Missouri State||58****|
|Northwest Missouri State||20|
|Northwest Missouri State||41|
|Northwest Missouri State||20*|
- "1995-1999 Carson-Newman Schedules". College Football Warehouse. cfbdatawarehouse.com. Archived from the original on 2014-01-11. Retrieved January 10, 2014.
- "1999 NCAA Division II National Football Championship Bracket" (PDF). NCAA. NCAA.org. p. 14. Retrieved January 10, 2014.