The 1999 Stephen F. Austin Lumberjacks football team was an American football team that represented Stephen F. Austin State University as a member of the Southland Conference during the 1999 NCAA Division I-AA football season. In their first year under head coach Mike Santiago, the team compiled an overall record of 8–3, with a mark of 6–1 in conference play, and finished as Southland co-champion.

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