During the Civil War, the lights were switched to intermittent operation. The lenses were removed for safekeeping by Confederate authorities. Union forces seized the city of Fernandina Beach in March 1862. They took over the lighthouses and Fort Clinch. It is unclear when the North Range lighthouse was destroyed, but it is clear that the tower did not survive the war.
Another Amelia Island North Range Light was built in 1872. This is the one pictured below in a National Archives photograph.
Other changes were made to the station over the next few years. A brick oil house was built, and hundreds of feet of sand fence were erected to try to halt moving sand dunes that threatened the dwelling. Finally, in 1899, the range was completely discontinued in March 1899, its function being replaced by additional buoys marking the channel.
Surveys of the area show an "old lighthouse" along the north shore in 1924. It is unknown when the lighthouse was finally destroyed, but today, no trace of the lighthouse remains.