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.

Date	Time	Opponent	Site	TV	Result	Attendance
August 31	7:00 pm	Hofstra*	Kenneth P. LaValle Stadium Stony Brook, NY (Battle of Long Island)	FSNY	L 17–8	5,626
September 9	1:00 pm	at Georgetown*	Multi-Sport Field Washington, DC		L 7–0	1,950
September 16	12:00 pm	at No. 1 New Hampshire*	Cowell Stadium Durham, NH		L 62–7	7,395
September 23	1:00 pm	at No. 9 UMass*	Warren McGuirk Alumni Stadium Hadley, MA		L 48–7	9,001
September 30	1:00 pm	at Monmouth	Kessler Field West Long Branch, NJ		W 36–17	2,531
October 7	2:00 pm	Albany	Kenneth P. LaValle Stadium Stony Brook, NY (rivalry)		W 33-21	6,688
October 14	1:00 pm	at St. Francis (PA)	DeGol Field Loretto, PA		W 30–20	716
October 21	1:00pm	Sacred Heart	Kenneth P. LaValle Stadium Stony Brook, NY		W 38–21	3,136
October 28	1:00 pm	Robert Morris	Kenneth P. LaValle Stadium Stony Brook, NY		L 21–6	1,893
November 4	1:00 pm	at Wagner	Wagner College Stadium Staten Island, NY		W 45–9	2,417
November 11	12:00 pm	at Central Connecticut	Arute Field New Britain, CT		L 35–32	2,587
*Non-conference game Homecoming Rankings from The Sports Network Poll released prior to the game All times are in Eastern time

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