Construction of the 67-foot tower was started in 1855. The fourth-order Fresnel lens was lighted in 1856, to mark the natural Gulf pass to Aransas and Corpus Christi Bays by way of Lydia Ann Channel.
Some sources say the channel was named for the daughter of the first keeper, but local historians believe it was named for Lydia Ann Dana Hastings Hull Wells, wife of James B. Wells, a veteran of the Texas Revolution who settled on St. Joseph Island and raised cattle there until his death in 1880.
The station was originally directly behind the pass, but the pass shifted south as much as 200 feet per year until it was stabilized by the construction of the first jetties in the 1880's.
During the Civil War (in 1861), Confederate soldiers removed the lens and buried it in the nearby marsh to prevent its use by Union forces, its location was lost and it has never been recovered. In 1863, they tried to destroy the tower with 4 kegs of black powder. The explosion blew the top off the tower and it was said that the spiral iron staircase shot straight up into the air. Although most of the tower survived, the top twenty feet had to be rebuilt and a new lantern crafted after the war.
A hurricane in 1916 flattened the keeper's dwelling, walkways, oil house and outhouse. They had almost been rebuilt when another hurricane hit in 1919. The auxiliary structures existing today were built after the 1919 hurricane.
The lighthouse was decommissioned in 1952 and in 1955, it was sold to Everett Bohls of Austin for $25,000. The current owner is Charles Butt, owner of the HEB grocery chain.
The Aransas Pass Lighthouse was one of original Texas stations of the U. S. Lighthouse Service (merged into the Coast Guard in 1939). It is the second oldest lighthouse on the Texas coast and the oldest surviving structure in the Aransas Pass-Corpus Christi area.