|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.
Northwest Missouri State defeated Carson–Newman in the championship game, 58–52 after four overtimes, to win their second Division II national title.
The Harlon Hill Trophy was awarded to Corte McGuffey, quarterback from Northern Colorado.
|School||1998 Conference||1999 Conference|
|Alabama A&M||D-II Independent||SWAC (I-AA)|
|Albany||Eastern (D-II)||Northeast (I-AA)|
|Elon||D-II Independent||I-AA Independent|
|Grand Valley State||MIFC||GLIAC|
|Minnesota Crookston||NDCAC (NAIA)||NSIC|
|Minnesota Morris||D-II Independent||NSIC|
|Saginaw Valley State||MIFC||GLIAC|
|Saint Anselm||Program revived||Eastern (D-II)|
|St. Francis (IL)||MIFC (D-II)||MSFA (NAIA)|
|Stony Brook||Eastern (D-II)||Northeast (I-AA)|
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*|