The 2006 Stephen F. Austin Lumberjacks football team represented Stephen F. Austin State University as a member of the Southland Conference during the 2006 NCAA Division I FCS football season. Led by second-year head coach Robert McFarland, the Lumberjacks compiled an overall record of 4–7 with a mark of 4–2 in conference play, tying for second place in the Southland. Stephen F. Austin played home games at Homer Bryce Stadium in Nacogdoches, Texas.
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