Interstate 10 and U.S. 90 run east and west through the county. Several state roads run north, providing access to the state of Georgia, and south to Gainesville, Orlando, and Tampa.
CSX Transportation offers rail service on a main tract route east and west through Macclenny.
Jacksonville International airport is 40 minutes from Baker County, Lake City Municipal Airport is 30 minutes away, and two other airfields, Craig and Herlong, are located in Jacksonville. Baker County also has two private airfields.