Not long after, he was made a lieutenant colonel in the 20th Massachusetts Volunteer Infantry, known as the "Harvard Unit" due to the number of graduates in this group.

He would serve under William Raymond Lee, and alongside Henry Livermore Abbott, Oliver Wendell Holmes Jr., and Paul Joseph Revere.

[2] On May 4, 1866,[3] President Andrew Johnson nominated Palfrey for the award of the honorary grade of brevet brigadier general, to rank from March 13, 1865, for gallant and meritorious services during the war,[4] The U.S. Senate confirmed the award on May 18, 1866.

He published A Memoir of William F. Bartlett (1879); Antietam and Fredericksburg, in the "Campaigns of the Civil War Series" (1882);[5] and contributed to the first volume of Military Papers of the Historical Society of Massachusetts and to the North American Review.

Palfrey's younger brother, John Carver Palfrey, was an 1857 graduate of the United States Military Academy and also served in the Civil War, eventually reaching the rank of Brevet Brigadier General.