Little about Doherty's early life is available other than he was born in Canada in 1840. He was living in New York when war erupted. He joined a 90 day militia unit and was assigned as a private to Company A of the 71st New York on 20 April 1861. The 71st saw action at First Bull Run assigned to Colonel Ambrose Burnside's 2nd Brigade of Colonel David Hunter's 2nd Division. The 71st, along with Doherty, mustered out on 9 August 1861.
Two years later Doherty joined the 16th New York Cavalry and was assigned as a 1st lieutenant. The 16th was assigned to the Washington defenses for the duration.
On 24 April 1865, 10 days after Abraham Lincoln was shot in Ford's Theater, Doherty was ordered to report to the office of Lafayette C. Baker, chief of the National Detective Police (NDP) which would eventually become the US Secret Service. He was ordered to form a detachment to hunt down John Wilkes Booth, the identified slayer of Lincoln, and any co-conspirators. The detachment embarked upon the steamer John S. Ide and proceeded down the Potomac River landing at Belle Plain, Virginia. Two days later the 25 man detachment of the 16th NY accompanied by Luther Baker, the cousin of Lafayette Baker, and Everton J. Conger, both agents in the NDP, caught up with Booth and David E. Herold in a tobacco barn near Port Royal, Virginia owned by Richard H. Garrett. According to Doherty's report Herold surrendered and Booth was killed.
Doherty, for his effort, was promoted to captain and given a $5,250 reward. He remained in the cavalry. The 16th NY was merged with the 13th NY forming the 3rd New York Provisional Cavalry on 23 June 1865. The 3rd NY was mustered out on 21 September 1865. Seven months later Doherty joined the regular cavalry and was assigned to the 5th US Cavalry as a 2nd lieutenant on 19 April 1866. He was promoted to 1st lieutenant on 1 March 1867 and remained in the regular army until mustering out in late 1870. He died in 1897 and is buried in Arlington National Cemetery.