Cushing began his military career as a sergeant in the 6th Continental Regiment in January 1776. He was commissioned a 2nd lieutenant in the 1st Massachusetts Regiment in January 1777 and was promoted to 1st Lieutenant in January 1778. He was taken prisoner in May 1781 and was later exchanged. He was breveted to the rank of captain in September 1783. In 1783 Cushing became an Original Member of the Massachusetts Society of the Cincinnati. Following the British evacuation of New York City in November 1783, the bulk of the Continental Army was discharged. Cushing was retained in Jackson's Continental Regiment, commanded by Brevet Brigadier General Henry Jackson, and was one of the last officers to be discharged from the Continental Army when the regiment was disbanded on June 20, 1784.
Later military career
On March 4, 1791 Cushing was commissioned a captain in the 2nd Infantry Regiment. On March 3, 1793 he was commissioned as a major in the 1st Sublegion. From February 27, 1797 to May 22, 1798 he served as Adjutant and Inspector General of the Army. In 1799, he commissioned artist James Peale to create a miniature portrait of himself. On June 15, 1800 he was re-appointed as Adjutant and Inspector General and held the office until April 2, 1807. From 1800 to 1807 he resided in Washington, D.C.. Cushing was promoted to lieutenant colonel of the 2nd Infantry on April 1, 1802. He was promoted to colonel of the same regiment on September 7, 1805. In early 1811, on the order of Brigadier General Wade Hampton I, Cushing was arrested and court martialed on charges of disobedience to orders and misuse of government funds. The court-martial first met on April 26, 1811 in Baton Rouge, Louisiana and was presided over by Colonel Alexander Smyth, with Winfield Scott appointed as the judge advocate. It lasted over a year and on May 5, 1812, Cushing was acquitted of most charges, and received only a written reprimand for the minor charges of which he was convicted.
Cushing was promoted to the rank of brigadier general on July 2, 1812. During the War of 1812, he served as Adjutant General of the Army from July 6, 1812 to March 12, 1813. He was then assigned as commander of Military District Number 1 with his headquarters at Boston. After the war's end, he retired from the Army on June 15, 1815.
Later life
In January 1816 Cushing was appointed collector of customs for the port of New London, Connecticut, succeeding Jedediah Huntington. In 1817, Cushing fought a duel with Virginia congressman William J. Lewis and was saved when the bullet struck his watch. The two resolved their differences, and Lewis, stepping up to the general, said: "I congratulate you, general, on having a watch that will keep time from eternity." Cushing died in New London in 1822. He was originally buried in the Second Burial Ground in New London but his remains were later relocated to the Cedar Grove Cemetery in the same city.