During the late 17th Century, the area was a staging ground for raids between English and French colonies.
Whitehall was first called "Skenesborough" in 1759 when it was settled by a land grant to a British officer, Philip Skene (1725-after 1785), who later returned to England, and who was subsequently declared an enemy of the State of New York for his land dealings. During the French and Indian War, the town was one of two major routes connecting the English and French Colonies.
During the American Revolution, the village, Skenesborough, was captured by American forces in 1774. Benedict Arnold under Philip Schuyler built a fleet of vessels to confront British forces at Valcour Island (thus the claim that this is the birthplace of the US Navy). The surviving American vessels returned here to be destroyed to keep them from falling into enemy hands. The next year John Burgoyne led his forces through this area en route to the Battle of Saratoga. After the war, the town's name was changed to Whitehall.
During the second half of the 19th Century, the silk industry grew important in the town.
Because of the actions in 1775 and 1776, the legislature of the State of New York in 1960 declared Whitehall to be the birthplace of the United States Navy. (They did not include Benedict Arnold as its creator.)