The 2003 Bethune–Cookman Wildcats football team represented Bethune–Cookman College (now known as Bethune–Cookman University) as a member of the Mid-Eastern Athletic Conference (MEAC) during the 2003 NCAA Division I-AA football season. Led by seventh-year head coach Alvin Wyatt, the Wildcats compiled an overall record of 9–3, with a mark of 6–2 in conference play, and finished second in the MEAC. Bethune–Cookman advanced to the NCAA Division I-AA Football Championship playoffs, where the Wildcats lost to Florida Atlantic in the first round.

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