With the start of the American Revolution, Scammell became a major in the 2nd New Hampshire Regiment, which was in Sullivan's Brigade, and after the Siege of Boston was sent with them to reinforce the Continental Army units in the Invasion of Canada. Sullivan's force returned to Fort Ticonderoga by mid July 1776, and by August Scammell had been assigned as Aide-de-Camp to Sullvan. But in September he was ordered to Assist Col George Reid in New York City and fought at the Battle of Long Island. In October 1776 he was appointed Assistant Adjutant General for Charles Lee's Division. In November 1776, Scammell was promoted to colonel. Then on 11 December 1776 he was given command of the 3rd New Hampshire Regiment.

Just two days after Burgoyne's surrender the regiment moved to winter quarters at Valley Forge where Scammell was appointed adjutant general of the Continental Army by Gen. George Washington. Scammell served in this capacity through 1780. In October 1780 Scammell was appointed as executioner to Major John André, a duty that weighed heavily on him. The result was a letter of Nov 16, 1780 to Washington requesting permission to resign his post and take command of a regiment of the line.

On September 30, 1781, while serving as Field Officer-of-the-Day, Scammell was wounded while reconnoitering recently abandoned British fortifications. He had become separated from his scouting party, encountered a party of British light dragoons, and was shot in the side (accounts differ as to whether this occurred before or after he surrendered). He was taken into Yorktown, but because of the gravity of his wound he was paroled to Williamsburg, only to die on October 6.