In the 1860s, with shipping commerce activity on the rise, a need grew for a lighthouse to define a clear channel. In June 1866, $6000 was allocated to create a day beacon on the Stepping Stones reef and a lighthouse near Hart Island about 1 ¼ miles north. When the property on Hart Island became difficult to obtain, the Lighthouse Board changed the lighthouse location to Stepping Stones.
Construction was begun by A.D. Cook in late 1875 using Irish bargemen and stone masons from Throgs Neck. The foundation of the tower was built directly over a large rock which just broke the surface at low tide. 900 tons of boulders was barged to the site between 1875 and 1878. The dwelling was completed in January 1877. The light was first turned on the evening of March 1, 1877 with Findlay Fraser as the first keeper. The original optic was a Fifth Oder Fresnel lens showing a fixed red light.