The Unincorporated Village of Port Jefferson is located within the town of Brookhaven on the North Shore of New York's Long Island. Port Jefferson Harbor is about 63 nautical miles (93 kilometers or 58 miles) east-northeast of the Port of New York. Sailing around Long Island, Port Jefferson Harbor is over 190 nautical miles northeast of Bay Shore Harbor on the south side, while it is only 30 kilometers (19 miles) from Bay Shore Harbor by land. The 2010 US Census reported a population of 7,750 in Port Jefferson Harbor.

The original inhabitants of Port Jefferson Harbor were the Setauket (or Setalcott) who lived in a village on the coast. The Setauket lived in wigwams while other tribes lived in tee-pees or long houses. Before Europeans came to Port Jefferson Harbor, it was a "royal residence" for Setauket leaders.

In 1655, five New Englanders traded goods like coats, hatchets, needles, knives, and other goods to the Setauket sachem Warawakmy in exchange for about 77 square kilometers (30 square miles) that would eventually contain Port Jefferson Harbor. Until the early 1700s, Port Jefferson Harbor was a small village called Drowned Meadow, and it had just five homes.

During the 18th Century, however, Port Jefferson Harbor grew as a ship-building community. Recognizing that Drowned Meadow was not a good name for a ship-building center, local leaders changed the name to Port Jefferson, after the United States' third President, Thomas Jefferson, in 1836. By the late 19th Century, Port Jefferson Harbor had become an important whaling port.

At one time, showman P.T. Barnum owned land in Port Jefferson Harbor, planning to make it the home base of his circus. When Port Jefferson Harbor residents blocked his plan, he sold his land. Barnum Avenue now occupies some of the land that Barnum owned, and one of the boats owned by the Bridgeport & Port Jefferson Ferry is named the P.T. Barnum.

The Village of Port Jefferson was formally incorporated in 1964. Containing several historic buildings, the Port Jefferson Village Historic District was listed in 2005 on the National Register of Historic Places. Recognized separately on the Register are the Bales Shipyard and First National Bank of Port Jefferson Harbor.

Since the early 1990s, Uptown Port Jefferson Harbor and Port Jefferson Station have been a popular destination for immigrants from Mexico, El Salvador, and the Dominican Republic.

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