The 2006 Jacksonville Dolphins football team represented Jacksonville University as a member of the South Division of the Pioneer Football League (PFL) during the 2006 NCAA Division I FCS football season. Led by ninth-year head coach Steve Gilbert, the Dolphins compiled an overall record of 4–6 with a mark of 4–3 conference play, and placed fourth in the PFL. Jacksonville played home games at D. B. Milne Field in Jacksonville, Florida.
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