The light was built to replace the Cape Henlopen Beacon, which was rapidly deteriorating at the time and was taken out of service later that same year.

Construction began in 1885 and a temporary light on a wooden frame was placed near the building site during the process.

The tower was fitted with a fourth-order Fresnel lens—which is still in the lighthouse to this day—and also included one red sector in order to warn vessels approaching the nearby Hen and Chickens Shoal.

Shoaling at Cape Henlopen gradually reduced the significance of the light and the Harbor of Refuge Light began to serve mariners in a more practical way at its location on the outer breakwater, much closer to the mouth of the Delaware Bay.

In 2004 the Authority and the Delaware River and Bay Lighthouse Foundation, a non-profit, volunteer organization, entered into a contract whereby the Foundation became advisors on the preservation to be undertaken by the Authority and were responsible for tours and educational activities.