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Decatur County was created in 1823 from portions of Early County. The county was named in honor of Commodore Stephen Decatur who defeated the Barbary Coast pirates at Tripoli in 1815. Bainbridge, the county seat, was named for Commodore William Bainbridge, commander of the U.S. Constitution, "Old Ironsides."

The Decatur County area was the site of several battles between Indians and early settlers. In the early 1700s, both the Spanish and English fought with Creek Indians. In 1818, General Andrew Jackson led troops from Tennessee, Kentucky, and Georgia to victory over the Seminole Indians.

Decatur County is divided by the Flint River, which flows to meet the Chattahoochee. Together they form the Apalachicola River which flows to the Gulf of Mexico. At the junction of the two rivers, the Jim Woodruff Dam forms Lake Seminole. A system of locks at the dam allows barge traffic to travel between the inland port at Bainbridge and the Gulf of Mexico.