When the Marion Rifles, a militia unit was formed in Marion County, John was elected Captain of the company. He enlisted, together with the other members of his unit, on 18 Apr 1861 and the unit was re-designated as A Company of the 5th Virginia Infantry Regiment. He and his company fought at First Manassas. In April of 1862, with the reorganization of the army, Funk was elected Lieutenant Colonel of the regiment then, after Colonel Baylor was killed leading the brigade at Second Manassas, Funk became Colonel of the regiment. When Brigadier General Paxton was killed at Chancellorsville, he temporarily commanded the brigade as the senior Colonel. He reverted to command the regiment when Brigadier James A. Walker ("Stonewall Jim") was assigned to command the brigade on 19 May. He fought at Culps Hill at Gettysburg. When the brigade was overwhelmed at the Mule Shoe on 12th May 1864, Funk was put in nominal command of the remnants of the Stonewall Brigade, while Col. William Terry (who was nearly a full year junior in seniority to Funk) was promoted to command the full brigade of the remnants of the rest of the division. Funk would serve with the "Stonewall Regiment" until he was mortally wounded at the Third Battle of Winchester, 19 Sep 1864. He died of his wound at his father's home 2 days later on 21 Sep 1864.
COL Funk is buried next to his brother in the Mount Hebron Cemetery in Winchester, Virginia.
