In 1673, construction began on the massive fortress of Castillo de San Marco. The fort, which is still standing, was made from limestone, crushed oyster shells and coral. This mixture, though seemingly soft for a bastion, absorbed cannon fire without cracking much better than a fortress made of stone would, and it provided St. Augustine with a center of defense. At the same time the Castillo de San Marco was built, a light tower was built to replace the watchtower with the same limestone, crushed shells and coral components.

In 1821, Spain ceded Florida to the United States. With the new government's financing now available, the grand jury of eastern Florida wrote President James Madison and asked for a new lighthouse in St. Augustine. In 1823, a $5,000 government grant was established and the current limestone tower was converted by contractor Elias Wallen into Florida's first lighthouse by 1824.

During the Civil War, Confederate sympathizers removed the lens in St. Augustine's light tower. The tower was not re-lit again until 1867.

During the next 30 years, mariners constantly complained that the light tower did not provide the visibility they needed. After a series of fruitless corrective actions, coupled with the increasing threat of land erosion near the lighthouse, the lighthouse board provided new funds for a new lighthouse to be built in 1871.

Paul Petz, who designed the Library of Congress, undertook the building of this new lighthouse and created a 165-foot tower with a first-order Fresnel lens. The new lighthouse was completed in 1874.

In 1898, St. Augustine's lighthouse was used as a lookout tower in the Spanish-American War. The light keeper of St. Augustine's served as the lookout and had signal flags and a telephone line that ran to the customs house to send an alert if needed.

Likewise, the lighthouse had an involvement in both World Wars. It was dimmed in World War I so as not to aid German U-boats in finding American ships to sink.

In World War II, the tower was used as a lookout as a team of light keepers worked around the clock from the top of the tower.

More recently, a nearly century-long lease agreement with St. Johns County was signed with the Junior Service League of St. Augustine in 1982, and the massive restoration of St. Augustine Lighthouse was undertaken to restore the lighthouse to its former glory. This process started with the Junior Service League obtaining placement for this grand lighthouse on the National Register of Historic Places.

Today the U.S. Coast Guard tends to this lighthouse, which is still an active guide to navigation.