European explorers first arrived in 1562, when French explorer Jean Ribault charted the St. Johns River.The French established the first European settlement at Fort Caroline two years later, however on September 20, 1565, a Spanish force attacked Fort Caroline from the nearby Spanish settlement of St. Augustine, and killed all the French soldiers (except Catholics). The Spanish renamed it Fort San Mateo. Two years later, the French recaptured the settlement from the Spanish and slaughtered all of the Spanish defenders. After the initial destruction of Fort Caroline, St. Augustine became the most important settlement in Florida.

During the Civil War, Jacksonville was a key supply point for hogs and cattle being sent north to Confederate soldiers. The city was blockaded by the Union and changied hands several times during the war. Though no battles were fought in Jacksonville, the city was left in disarray after the war. During Reconstruction and the Gilded Age, Jacksonville and nearby St. Augustine became popular winter resorts. Visitors arrived by steamboat and later by railroad. The city's tourism was dealt major blows in the late 1800s by yellow fever outbreaks and the extension of the Florida East Coast Railroad to south Florida.

On May 3, 1901, downtown Jacksonville was ravaged by a fire that was known as the "Great Fire of 1901." one of the worst disasters in Florida history, destroying the business district and rendering 10,000 residents homeless in the course of eight hours. It is said the glow from the flames could be seen in Savannah, Georgia, and smoke plumes in Raleigh, North Carolina. Famed New York architect Henry Klutho was a maor force in the reconstruction of the city.

Following the reconstuction from the fire, the city had a brief period as a major film producing center, before Hollywood came to dominate the industry. Since then, Jacksonville has become the headquarters of many banking and insurance companies, resulting in a thriving business district. Jacksonville is also home to three major Naval bases established during World War II.