A lighthouse was established on the westernmost point of West Sister Island in 1848 to mark the west end of the South Passage through Lake Erie’s Bass Islands. The tower was renovated in 1868, and a keeper's dwelling was constructed. It is not clear what the renovation entailed, but the end result was the tower as it appears today. Standing on a stone foundation, the conical limestone and brick tower rises to a height of 55 feet. Originally crowned with a fourth-order Fresnel lens in 1848, the light performed its daily function undisturbed for almost ninety years.

John Edson was keeper of the lighthouse until his death at the station one fall. Edson's son-in-law, Martin Goulden, left his own wife and Mrs. Edson and set out in the station's boat for Toledo to obtain a coffin. Mid-journey, a sudden blizzard started to rage and Goulden sought refuge at the lighthouse on Turtle Island. The following day, Nathan Wint Edson, keeper of the Turtle Island Lighthouse, decided to accompany Goulden to Toledo, but after traveling just a mile from the island, their boat was crushed by lake ice, plunging them into the frigid water. They attempted to make their way back to the island, but their bodies were later found frozen fast in the ice.

Harrison Haynes was appointed the replacement keeper at West Sister Island, and in his spare time, he raised a flock of turkeys on the island. Shortly before Thanksgiving one year, the family killed and dressed 75 plump turkeys. The Swansea tug was due the next morning to take the turkeys to market, but the ice surrounding the island stopped the tug just within the vision of the lighthouse family. Haynes' daughter recalls that it was turkey, morning, noon, and night that winter, and since then she has not been able to take a single bite of turkey.

The West Sister Island Lighthouse was automated in 1937, at which time the keepers dwelling, built in 1868, was abandoned. A 300mm lens and solar power cell took the place of the Fresnel lens, shining from a 57-foot focal plane. Also in 1937, President Franklin D. Roosevelt established the island "as a refuge and breeding ground for migratory birds and other wildlife." The West Sister Island National Wildlife Refuge would protect the largest wading bird nesting colony on the Great Lakes.

Ironically, after being established as a wildlife refuge, West Sister Island was used by the United States Army for artillery practice during World War II. While neither the wildlife population nor the lighthouse suffered significant damage, the keeper's quarters were destroyed, and it is reported that fuel tanks, jettisoned by dive bombers, can still be found on the island.

In January 1975, the government designated 77 of West Sister Island's 82 acres as wilderness. The United States Fish and Wildlife Service (USFWS) maintains ownership of this portion, while the USCG owns the lighthouse and the remaining five acres.

West Sister Island Lighthouse is still an active aid to navigation, and it is among the oldest lighthouses to survive on the Great Lakes. It is not open to the public, as visitors would pose a threat to the refuge's vital nesting area. The island is home to many varieties of birds, including great blue herons, great egrets, black-crowned night herons and double crested cormorants.