At the outbreak of the Civil War, Roberts was Major of the 3rd U.S. Cavalry. He served in Arizona and New Mexico in 1861 and 1862. He was promoted to Brigadier General of Volunteers on June 16, 1862, and assigned to General John Pope's staff as Inspector General and Chief of Cavalry. He saw action at Cedar Mountain, Rappahannock Station, Sulphur Springs and the Second Battle of Bull Run. After Bull Run, he was manipulated by Secretary of War Edwin M. Stanton to prefer charges of disloyalty, disobedience and misconduct against Fitz John Porter, and testified at the subsequent court-martial, which ruined Porter's career.