The 2006 Humboldt State Lumberjacks football team represented Humboldt State University—now known as California State Polytechnic University, Humboldt—as an independent during the 2006 NCAA Division II football season. Led seventh-year head coach Doug Adkins, the Lumberjacks compiled a record of 9–1. The team outscored its opponents 324 to 194 for the season. Humboldt State played home games at the Redwood Bowl in Arcata, California.

The Great Northwest Athletic Conference (GNAC) did not sponsor football for the 2006 and 2007 seasons.

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