Marshall served in the Union Army during the American Civil War as Aide-de-camp to General John Pope, from August, 1861, to July 22, 1865, serving in Missouri Operations, August, 1861, to April, 1862, the Advance upon and Siege of Corinth, April to May, 1862, and the Northern Virginia Campaign, July to September, 1862. Promoted Colonel, Staff – Additional Aide-de‑Camp, June 30, 1862, to July 28, 1865.