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. 
 Schedule
 | Date | Time | Opponent | Site | TV | Result | Attendance | 
|---|
| August 31 | 7:00 pm | Hofstra* |  | FSNY | L 17–8 | 5,626 | 
 | September 9 | 1:00 pm | at Georgetown* |  |  | L 7–0 | 1,950 | 
 | September 16 | 12:00 pm | at No. 1 New Hampshire* |  |  | L 62–7 | 7,395 | 
 | September 23 | 1:00 pm | at No. 9 UMass* |  |  | L 48–7 | 9,001 | 
 | September 30 | 1:00 pm | at Monmouth |  |  | 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) |  |  | 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 |  |  | W 45–9 | 2,417 | 
 | November 11 | 12:00 pm | at Central Connecticut |  |  | L 35–32 | 2,587 | 
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 [1][2] 
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