Trafton was born in Bangor, Maine (then a district of Massachusetts). His father (also Mark Trafton, 1785-1857) was Capt. of the cavalry company of the local militia, and participated in the Battle of Hampden in 1814, which resulted in the British sacking of Bangor. Later a militia General, the elder Trafton also served in the Aroostook War, opened and ran the U.S. Customs House in Fort Fairfield, Maine, and founded the nearby town of Limestone. Trafton's mother was the daughter of Jacob Dennett, one of Bangor's original settlers.
The younger Trafton studied at Kent's Hill Seminary, and was ordained pastor of the Methodist Episcopal church in Westfield, Massachusetts. In the early 1850s he traveled in Europe and published his letters home as Rambles in Europe: In a Series of Familiar Letters (Boston, 1852). The volume is dedicated to George W. Pickering, a cousin and prominent merchant in Bangor, Maine, who may have financed the trip. Trafton never lost touch with his home town of Bangor, returning to speak at its centennial celebration in 1869.
Trafton was elected as the candidate of the American Party (aka the Know-Nothing Party) to the Thirty-fourth United States Congress (March 4, 1855-March 3, 1857). All eleven U.S. Representatives in the Massachusetts delegation were members of the American Party, including Speaker of the House Nathaniel P. Banks. According to his New York Times obituary, Trafton "had been an active leader in the anti-slavery reform, and while a member of Congress he secured the cordial hate of his opponents by his bold assaults upon the slave power". He was an unsuccessful candidate for reelection in 1856 to the Thirty-fifth Congress, and resumed his ministerial duties as pastor of a church in Mount Wollaston, Massachusetts. He was also pastor of the Trinity Methodist Episcopal Church in Charlestown.