When Europeans first arrived in this area in the 16th century, the inhabitants were Timucuan Indians. In 1774, traveling botanist William Bartram visited Seminole Indians nearby. In the 1850’s a town called Deer Hammock was established here, probably in anticipation of the construction of the Florida Railroad from Fernandina to Cedar Key. Upon completion of the railroad to Deer Hammock in 1859, the name of the town was changed in honor of James T. Archer, Florida’s Secretary of State 1845-49 and advocate of internal improvements. The Archer post office was established the same year. In May, 1865, the remnants of the Confederate treasury, removed from captured Richmond and conveyed by baggage train into Florida, were hidden at Cotton Wood, the Archer plantation of David Yulee, just prior to Union seizure at Waldo.

In the contested presidential election of 1876, the votes of the Archer precinct for the Republican candidate were among those challenged but allowed to stand, thus securing the victory of Rutherford B. Hayes over Samuel J. Tilden. The town of Archer was incorporated in 1878. Among new arrivals in the 1880’s were Quakers who planted extensive orange groves using avenues of oaks as windbreaks. The freezes of 1886 and 1894-95 killed the orange trees, but the oaks survived to shade the city streets. Archer’s oldest surviving industry is the Maddox Foundry, established in 1905 by H. Maddox and operated by his descendants.