Boothbay Harbor is a census-designated place (CDP) comprising the densely populated center of the town of Boothbay Harbor in Lincoln County, Maine, United States.

To the northwest the CDP is bordered by the inlet stream of Mill Cove, running northeast to Maine State Route 27.

To the northeast, the CDP is bordered by Maine State Route 96 (Ocean Point Road) and to the east it extends to Meadow Brook.

Lobster Cove Road forms the southeasternmost extent of the CDP.

According to the United States Census Bureau, the CDP has a total area of 0.85 square miles (2.2 km2), all land.