In 1777 he had received the appointment of brigadier-general, and was put in command of the first brigade of the provincial troops of New Hampshire, acting in concert with General Stark, who commanded the other. At that time General Burgoyne was on the flood tide of his military glory in the north, spreading consternation far and wide. He was first checked in his triumphant career by General Stark, at Bennington, Vermont. General Whipple, about the same time, joined General Gates with his brigade, and was in the bloody battles of Stillwater and Saratoga, where the palm of victory was attributed in a great measure to the troops under his command. In the consummation of the brilliant victory over the British army under Burgoyne, which shed fresh lustre on the American arms, General Whipple contributed largely. Colonel Wilkinson and he were the officers who arranged and signed the articles of capitulation between the two commanders. He was also selected as one of the officers to conduct the conquered foe to Winter Hill, near Boston. His faithful negro, whom he manumitted at that time, participated in all the perils of his old master, and seemed as much elated with the victory as if he had been the commander-in-chief.
In 1778, General Whipple was with General Sullivan at the siege of Newport, which was necessarily abandoned in consequence of the failure of the anticipated co-operation of the French fleet under Count D’Estaing, which was unexpectedly injured in a gale of wind. A safe and fortunate retreat was effected in the night, which saved that portion of the American army from total destruction.
In 1780 General Whipple was appointed a commissioner of the board of admiralty by Congress, which honour he did not accept, preferring to serve in the legislature of his own state, to which he had just been elected, and in which he continued for a number of years.
In 1782 he was appointed by Robert Morris financial receiver for the state of New Hampshire, which conferred upon him the highest eulogium for integrity and honesty. The office was arduous, unpopular, and irksome, but he performed its duties faithfully until the 2nd of July, 1784, when he resigned. In conjunction with the many honourable stations he filled, he was appointed a judge of the superior court on the 20th of June, 1782, and on the 25th of December, 1784, was appointed a justice of the peace and quorum throughout the state, which offices he held to the day of his death. He was also one of the commissioners on the behalf of Connecticut, who met at Trenton to settle the unpleasant controversy between that state and the commonwealth of Pennsylvania, relative to the lands in Wyoming valley. In all the multiform public duties that devolved upon him, he acquitted himself nobly, and retained, to his last moments, the entire confidence of his country. He possessed a strong and analyzing mind, a clear head, a good heart, and deep penetration of thought. In all the relations of private and public life, from the cabin boy up to the lofty pinnacle of fame on which he perched, he maintained a reputation pure as the virgin sheet. During the latter part of his life, he suffered much from disease in his chest, which terminated his useful and patriotic career on the 28th of November, 1785. Agreeably to his request before his death, his body underwent a post-mortem examination. His heart was found ossified; the valves were united to the aorta, and an aperture, not larger than a knitting needle, was all that remained for the passage of the blood in its circulation. This accounted for his having often fainted when any sudden emotion excited a rapid flow of his life stream.