The 2006 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 2006 NCAA Division I FCS football season. Led by 10th-year head coach Alvin Wyatt, the Wildcats compiled an overall record of 5–6, with a mark of 3–5 in conference play, and finished seventh in the MEAC.

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