The 2006 Northern Illinois Huskies football team represented Northern Illinois University as a member of the West Division of the Mid-American Conference (MAC) during the 2006 NCAA Division I FBS football season.

Led by 11th-year head coach Joe Novak, the Huskies compiled an overall record of 7–6 with a mark of 5–3 in conference play, tying for third place in the MAC's West Division.

Northern Illinois was invited to the Poinsettia Bowl, where they lost to TCU.

The team played home games at Huskie Stadium in DeKalb, Illinois.

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