The 2003 Stony Brook Seawolves football team represented Stony Brook University as a member of the Northeast Conference (NEC) during the 2003 NCAA Division I-AA football season. Led by 20th-year head coach Sam Kornhauser, the Seawolves compiled an overall record of 6–4 with a mark of 4–3 in conference place, tying for third place in the NEC. Stony Brook played home games at Kenneth P. LaValle Stadium in Stony Brook, New York.
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