Enlisting in the Union Army in May 1861, he received a commission as an officer with the 9th New York Volunteer Infantry Regiment, popularly known as "Hawkins' Zouaves", and later the IX Army Corps where he served under General Benjamin Butler at the Battle of Big Bethel and Hatteras Inlet expedition. In 1862, he accompanied the Army of the Potomac in General Ambrose Burnside's Roanoke expedition and took part in the Battles of Hatteras Inlet, Roanoke Island, South Mountain, Antietam and Fredericksburg. Twice wounded during the campaign, Jardine was promoted to the rank of major for "gallant conduct" and briefly commanded the 89th New York Infantry Regiment.