Middleburg began in the 19th century with several different names. It was first known as Clark's Ferry from the 1820s to 1833. The name derived from Asa Clark who ran the ferry until 1828. In 1828 the Black Creek Methodist Church was founded by Isaac Boring but the frontier Methodist society met in their own homes until the Methodist United Church was built in 1847. Fort Heilman protected settlers at Clark's Ferry where it was the "principal depot for the east coast of Florida. During the Seminole Wars Fort Heilman was used as a quartermaster workshop and storage depot but was abandoned after the war in 1841. From 1833 to 1850 the area was then known as Gary's Ferry after Samuel Y. Gary. On September 8, 1853 the area was finally called Middleburg. The new town traded in timber, citrus fruits and crops from farmland. When Clay county was created in 1858 Middleburg became the temporary county seat until 1874.
The 4th Massachusetts Cavalry had a small skirmish before raiding Middleburg during the American Civil War on October 23, 1864. The next day the 4th Massachusetts Cavalry set fire to a number of buildings and a hotel. The Federals retreated across Black Creek burning a bridge in the process. The Florida 2nd Cavalry caught up with the retreating 4th Massachusetts Cavalry in a skirmish at Halsey's Plantation.
The population numbered 700 in 1890. In 1895, a big freeze and lessening of the river trade caused the city to decline again.