Fernandina Beach is located on Amelia Island, in Nassau County. It is the county seat of Nassau County. The area was first inhabited by the Timucuan tribe.

Known as the "Isle of 8 Flags," it has had, in succession, the following flags flown over it since 1562: France, Spain, Great Britain, Spain (again), the Patriots of Amelia Island, the Green Cross of Florida, Mexico, the Confederate States of America, and the United States. It is the only municipality in the United States that has flown eight different national flags.

At the time of the 2000 census, Fernandina Beach's population was 10,549. In 2004, the population recorded by the U.S. Census Bureau was 11,241.