The 2006 Stony Brook Seawolves football team represented Stony Brook University as a member of the Northeast Conference (NEC) during the 2006 NCAA Division I FCS football season. Led by first-year head coach Chuck Priore, the Seawolves compiled an overall record of 5–6 with a mark of 5–2 in conference place, placing in a three-way tie for second in the NEC. Stony Brook played home games at Kenneth P. LaValle Stadium in Stony Brook, New York.
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