The 52-year-old Bowden, the son of Florida State coach Bobby Bowden, brings a 111-53-2 record to North Alabama, which finished the 2008 season 12-2 and reached the semifinals of the Division II playoffs.
The school said it would introduce Bowden at a news conference Thursday.
Bowden replaces Mark Hudspeth, who left to become an assistant coach at Mississippi State.
Bowden, who won his first 20 games at Auburn in 1993-94, has been working as an analyst on Westwood One's college game of the week.
The family also includes Tommy Bowden, who quit as Clemson's coach at midseason in 2008 after a disappointing start.
Terry Bowden was a running back at West Virginia and served as a graduate assistant at Florida State while earning a law degree.
He was head coach at Salem College and Samford before taking over the Auburn program after the 1992 season. After an 11-0 season in 1993, the Tigers were 9-1-1 in 1994.
He resigned in 1998 the day before a game and said he had been pressured to quit. Auburn officials denied applying pressure on Bowden.
Terry Bowden
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