Immediately after President Abraham Lincoln’s call for volunteers at the beginning of the Civil War, Catlin raised a company of infantry and was appointed its captain. The unit, said to be “the first full company which enlisted in the North,” was mustered in on May 14, 1861, as part of Frederick Townsend’s 3rd New York Volunteer Infantry Regiment. Regarding the regiment’s participation in the Battle of Big Bethel on June 10, 1861, Townsend remarked: “There was no braver officer on that field than Captain Catlin.” Following the battle, the unit was stationed at Fort McHenry in Maryland. Isaac Catlin resigned his position in the 3rd New York on March 14, 1862, and rejoined the Army five months later, on August 2, with the 109th New York Volunteer Infantry Regiment. He began his service with the 109th as a first lieutenant but was promoted to lieutenant colonel only weeks later. Promoted to full colonel on July 29, 1864, he led the 109th New York in the Battle of the Crater at Petersburg, Virginia, the next day. During the battle, he was seriously wounded but returned to the field and continued to lead his regiment until being struck a second time. The second wound necessitated the amputation of his right leg. For this action, he was given a brevet promotion to major general on March 13, 1865, and awarded the Medal of Honor several decades later, on January 13, 1899.

Isaac Catlin was mustered out of the volunteer army on June 4, 1865, and joined the regular army as a captain on May 6, 1867. On that same date, he was given the regular army brevet ranks of major, for his actions at the Battle of the Wilderness, and lieutenant colonel, for his actions at Petersburg. He retired from the military on May 6, 1870, and was simultaneously promoted to colonel. While on the retired list he was again promoted, to brigadier general, on April 23, 1904. In his later years, Catlin split his time between homes in Brooklyn and Owego. He was a member of the New York Society of Colonial Wars. In January 1916 he suffered a stroke and died a week later, on January 19, at his apartment in Brooklyn’s Hotel St. George. Aged 80 at his death, he was buried at Arlington National Cemetery in Arlington County, Virginia.