Harkers Island was inhabited by the Coree Indians in the 16th century when European explorers first arrived. Originally know as Craney Island, Farniford Green was the first patent holder of the island in 1707. The island was purchased by Ebenezer Harker in 1730. Ebenezer had immigrated from England to Massachusetts. He arrived in Beaufort, NC to be appointed the whale oil revenuer for the area. Ebenezer built a plantation and boat yard on the island and lived there with his family until his death in 1800. He was the last sole landowner of the island.

After the San Ciriaco storm of 1899 people relocated to the island from the community of Diamond City. Many of them converted to the Latter Day Saints and soon outnumbered the members of the island's Methodist Episcopal Church. After the Smoot Hearings the relationship between the Mormons and the Islanders deteriorated. Islanders threw rocks and oyster shells through the windows of the LDS church and fired gunshots into the building. The church was burned to the ground in 1906 by arsonists. Today the Island has one of the highest percentages of Latter-day Saints per locality in North Carolina.

A bridge was built to the island in 1941. Much disagreement and discussion ensued about wanting a bridge and where it should be located. Many people wanted the bridge on the west end connected to the Town of Beaufort. The 1966 bridge and the 2003 bridge were built as before to connect the island to Straits.

Harkers Island was once in the Guinness Book of World Records as having the most churches per capita in the United States. The Harkers Island Rural Electric Authority was the first cooperative to supply electricity through a submarine cable.

Seavisions Charters has been an authorized guided boat tour operator at the Cape Lookout National Seashore since 2008.