The first fort was built by the British in the early 18th century for the same reason most British forts of this era were built ie. to guard an important port or city. Fort Macon protected the English city of Beaufort against pirates such as Blackbeard and Spanish invasions.

Construction of the present fort began in 1826. Named after state senator Nathaniel Macon, who procured the funds to build the facility. The fort was completed in 1834 as part of a chain of 38 coastal fortifications for national defense that were built between 1817 and 1865. Later occupied by the Union during the Civil War when the Confederate Army surrendered the fort after a non-stop barrage of shells in 1862.

Fort Macon was a federal prison from 1867 to 1876, garrisoned during the Spanish-American War and closed in 1903. Congress offered the sale of the fort in 1923, and the state purchased the land, making it the second state park. Restored by the Civilian Conservation Corps from 1934-35, the fort was garrisoned for the last time during World War II.