Whipple was born at Kittery, Maine, and educated at a common school studying how to be a merchant, judge, and a solider until he went off to sea. He became a Ship's Master by the age of twenty-three. In 1759 he landed in Portsmouth, New Hampshire, and in partnership with his brother established himself as a merchant. He married his first cousin Katherine Moffat some time around 1770 to 1771.
In 1775 he was elected to represent his town at the ProvincialCongress. 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.
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. He was buried in the Old North Burial Ground in Portsmouth, New Hampshire. In 1976, in conjunction with the American Bicentennial, his headstone was replaced by a local historical association.