In June 1861, Stannard was elected lieutenant colonel of the 2nd Vermont Volunteer Infantry. Some local residents claimed that he was the first Vermonter to volunteer for duty in the Civil War, based on his immediate reply by telegram to the governor's first call for troops. He fought with the 2nd Vermont at the First Battle of Bull Run in July 1861, successfully enough that he was offered command of the newly forming 3rd Vermont, but he turned it down because he thought he had not served long enough to qualify. During the Battle of Williamsburg in the Peninsula Campaign the following year, Brig. Gen. Winfield S. Hancock's report indicated that Stannard was responsible for securing a bridge that was crucial to the battle. A week after the campaign, on July 9, 1862, he was appointed colonel of the 9th Vermont Infantry.