As the American Civil War broke out he was, on the recommendation of Colonel Sumner, commissioned as First Lieutenant in the 5th U.S. Cavalry, one of the new regiments authorized by Congress.

His new regiment was attached to Thomas Francis Meagher's Irish Brigade the following November, and with it participated in the fierce fighting in which the Army of the Potomac was subsequently engaged.

At its head, Colonel Byrnes charged up the slope of Marye's Heights at the Battle of Fredericksburg, and after it, like the other regiments of the brigade, had been almost wiped out in the sanguinary conflicts at Chancellorsville and Gettysburg, he was sent back to Massachusetts to recruit its ranks during the winter and spring of 1863 and 1864.

Two weeks after assuming command, on June 3, 1864, Colonel Byrnes fell, mortally wounded, while leading the brigade during the attack on the entrenchments at Cold Harbor, Virginia.

His commission as brigadier general had just been made out by President Abraham Lincoln, but he was dead before it could be officially presented to him, and so the promotion never took effect.