The 1999 NCAA Division I-AA football season, part of college football in the United States organized by the National Collegiate Athletic Association (NCAA) at the Division I-AA level, began in August 1999, and concluded with the 1999 NCAA Division I-AA Football Championship Game on December 18, 1999, at Finley Stadium in Chattanooga, Tennessee.

The Georgia Southern Eagles won their fifth I-AA championship, defeating the Youngstown State Penguins by a score of 59−24.

[1] Atlantic 10 Conference – James Madison and Massachusetts Big Sky Conference – Montana Gateway Football Conference – Illinois State Ivy League – Brown and Yale Metro Atlantic Athletic Conference – Duquesne Mid-Eastern Athletic Conference – North Carolina A&T Northeast Conference – Robert Morris Ohio Valley Conference – Tennessee State Patriot League – Colgate and Lehigh Pioneer Football League – Dayton Southern Conference – Appalachian State, Furman, and Georgia Southern Southland Football League – Stephen F. Austin and Troy State Southwestern Athletic Conference – Southern * By team name denotes host institution

* By score denotes overtime

Source:[2]