Oil Company in Bellport, NY.

The land that is now Bellport was purchased along with what is now the hamlet of Brookhaven (then called Fireplace Neck) and western South Haven from the Unkechaug Indians in 1664 by settlers from nearby Setauket, who were attracted by the plentiful harvests of salt hay. The part that became Bellport was named Occumbomock Neck. Jonathan Rose was the first permanent settler in the 1680s, and by 1720 the Rose family owned much of Occumbomock Neck. In 1829, Captain Thomas Bell, a Scottish immigrant, bought land there. He sold sections of it, and by 1843 the village had 30 dwellings and 200 inhabitants. He changed the name to Bell-Port (now Bellport), envisioning a seaport, since Bellport was very close to the Old Inlet, a breach in the barrier island Fire Island, which gave Bellport easy access to the open ocean. With Colonel William Howell, Bell built a dock and a road to the dock. But the breach healed over, and Bellport instead became a tourist attraction, with wealthy visitors coming by railroad and then coach from New York City. Although all seven hotels eventually closed, the last in the 1950s, Bellport remained associated with wealthy New Yorkers, who eventually established year-round residences. After World War II, nearby Camp Upton was converted into Brookhaven National Laboratory, bringing in more, highly educated, year-round residents.

Bellport was incorporated as a village in 1910. On July 4, 1980, the Bellport Academy and Bellport Village Historic District were listed on the National Register of Historic Places.

On March 8, 1963, Bellport High School burned down. No one was killed, but 40 students and teachers were hospitalized. The replacement school was built in Brookhaven, but is still called Bellport High School.