Whipple was given his first commission by the New Hampshire Provincial Congress in 1777. At Saratoga, Whipple was placed in command of a brigade, consisting of four regiments of militia. Whipple commanded Bellow's regiment, Chase's regiment, Moore's regiment, and Welch's regiment. As a result of their meritorious conduct at the Battle of Saratoga, Whipple and Colonel James Wilkinson were then chosen by Major General Horatio Gates to determine terms of capitulation with two representatives of General John Burgoyne. Whipple then signed the Convention of Saratoga, the effective surrender of General Burgoyne and his troops. Whipple was then appointed along with several other officers to escort Burgoyne and his army back to Winter Hill, Somerville, Massachusetts. Whipple passed the news of the victory at Saratoga to Captain John Paul Jones, who informed Benjamin Franklin, who was in Paris at the time. News of the victory proved valuable to Franklin throughout alliance negotiations with the French. In 1778, Whipple followed his commanding officer, General John Sullivan to the Battle of Rhode Island, where he commanded Evans' regiment, Peabody's regiment, and Langdon's light horse regiment. After General Sullivan ordered retreat, Whipple and other officers resided in a house near the battlefield. The approaching enemy fired a field piece from a range of three-quarters of a mile. The shot first tore through a horse lashed outside the house before severely wounding the leg of one of Whipple's brigade majors, which later required amputation.