The village was founded in 1759 as "Skenesborough" by Captain Philip Skene of the British army. It was the first settlement at Lake Champlain and became an important trade center. It was on one of two routes between English and French colonies.
On May 9, 1775 Lieutenant Samuel Herrick, acting as an advance party for Ethan Allen's attack on Fort Ticonderoga surprised Major Skene and his small garrison. While he intended to use Skene's boats to ferry men across the lake, his party didn't arrive in time. Skene's schooner was used later to capture St. Johns.
In 1776, General Philip Schuyler built a small fleet of ships here. They were used by Benedict Arnold in the Battle of Valcour Island in October. The event led to Whitehall's modern-day claim to be the birthplace of the United States Navy. The surviving vessels returned to be destroyed to prevent their capture. General John Burgoyne led his forces southward through this area during the Saratoga Campaign.
During the War of 1812 the village was a ship building community supplying vessels for naval battles on Lake Champlain.