The first fort on this site was Abraham Shurte's Fort, a palisaded trading post that was burned down by pirates under Dixie Bull. The next fort on the site was Fort Pemaquid, which was destroyed in the Northwest Coast Campaign during King Philip's War.
Fort William Henry was built in 1692 during King William's War. The English constructed it to defend against the French and Wabanaki Confederacy of Acadia. The English built Fort William Henry as a fortress to protect the northern boundary of New England. Massachusetts government used one third of its budget to build the fort. Construction of the fort was ordered by Massachusetts GovernorSir William Phips and cost £20,000 to build. The English colonial militia leaderBenjamin Church assisted in the construction. The fort was built with walls that were 10 to 22 feet in height and a stone bastion which was 29 feet in height. The fort was armed with 20 cannon and a garrison of 60 soldiers. The fort was attacked by a combined force of French and Native Americans in the Siege of Pemaquid. The English were forced to surrender the fort and abandon the Pemaquid area. Benjamin Church avenged the destruction of the fort with the Raid on Chignecto against Acadia.
After Father Rale's War, Colonel David Dunbar, Surveyor-General of the King's Woods, rebuilt the fort in 1729–1730, renaming it Fort Frederick. During King George's War, Fort Frederick was attacked during the Northeast Coast Campaign by bands of Penobscot and Norridgewock. They took captive a woman, which alarmed the garrison but she escaped. The fort withstood two attacks in 1747. During the French and Indian War, the fort was decommissioned in 1759 after a new Fort Frederick was built on the Saint John River the previous year. In 1775, the town dismantled the fort to prevent it from becoming a British stronghold during the Revolutionary War. During the War of 1812, the waters off Pemaquid Point saw the capture of HMS Boxer by the USS Enterprise on September 5, 1813. The fort was occupied by the British twice during the war. The state acquired the site in 1902, and in 1908 rebuilt the tower of Fort William Henry under guidance of historian John Henry Cartland, using many original stones. In 1969, the fort was listed on the National Register of Historic Places. The entire state historic site was designated the "Pemaquid Archeological Site" National Historic Landmark District in 1993.