In 1862, Pingree enlisted in the Union Army to serve in the Civil War with the 1st Massachusetts Heavy Artillery Regiment (Company F). He fought on the front line during General Pope’s Northern Virginia Campaign and the Second Battle of Bull Run. The regiment he fought with was then ordered to defend Washington, D.C. until May 15, 1864, and then was sent to the front again. He fought with the Second Brigade of Tyler’s Division, Second Corps, which participated in battles at Fredericksburg Road (May 18), Harris Farm (May 19), and Spotsylvania Court House (May 19–21).