William Whipple was born at Kittery, Maine, and educated at a common school until his early teens, when he went off to sea. He became a Ship's Master by the age of twenty-one. In 1759 he landed in Portsmouth and, in partnership with his brother, established himself as a merchant.
In 1775 he was elected to represent his town at the provincial congress. In 1776 New Hampshire dissolved the Royal government and reorganized with a House of Representatives and an Executive Council. Whipple became a Council member, and a member of the Committee of Safety, and was elected to the Continental Congress, serving there through 1779.
In 1777 he was made Brigadier General of the New Hampshire Militia, participating in the successful expedition against General Burgoyne at the battles of Stillwater and Saratoga.
After the war he became an associate justice of the Superior Court of New Hampshire. He suffered from a heart ailment and he died by fainting from atop his horse while traveling his court circuit.