On August 28, 1862, Merrill enlisted in Company B, 4th Regiment Massachusetts Infantry (nine-month militia) and commissioned 1st lieutenant, September 1, 1862.

He mustered out of the service with the regiment August 28, 1863, at Camp Hooker in Lakeville, Massachusetts.

In 1875, Merrill was elected Commander of the Massachusetts Department, Grand Army of the Republic.

He was also a veteran companion of the Massachusetts Commandery of the Military Order of the Loyal Legion of the United States.

Merrill died February 17, 1900, in Lawrence, Massachusetts and is buried there in Bellevue Cemetery.