He reenlisted in the 11th Independent Battery, New York Light Artillery on September 18, 1861, for a period of three years. On August 26, 1862, he was captured with 19 other soldiers from the 11th IBNYA at the Second Battle of Bull Run also known as Second Manassas. During October and November 1862 he is listed with the 7th Detachment, 2nd Battalion, Paroled Prisoners, at Annapolis, Maryland. After returning to the 11th IBNYA in December 1862 he was promoted to Corporal on January 2, 1863. Corporal Shepard's unit was transferred to the Reserve Artillery and attached temporarily to Battery K, 1st New York Light Artillery. Shepard also saw action at Chancellorsville, Gettysburg and the Battle of Mine Run.