Newton is the county seat of Baker County. Baker County was established in 1825 and was designated the county seat in 1831. The county was named for John Baker, a Colonel during the Revolutionary War. The city was incorporated January 20, 1872 and named for Sergeant John Newton of South Carolina, a soldier in the Revolutionary War.

The Baker County courthouse in Newton, built in 1900, is listed on the National Register of Historic Places. The courthouse was restored in the mid-1990s after being flooded by Tropical Storm “Alberta.”