Moylan's first battle, the Battle of Wilson's Creek Missouri, was fought on August 10, 1861. Moylan also participated in the Battle of Fort Henry, Tennessee, on February 6, 1862, and in the Battle of Fort Donelson, Tennessee, on February 11–16, 1862. Then the Battle of Shiloh, Tennessee, April 6–7, 1862, and the Siege of Corinth, Mississippi, from April 29–May 30, 1862. On March 28, 1863, Moylan was promoted to the rank of second lieutenant in the 5th United States Cavalry. In this organization he fought in the Battle of Gettysburg, Pennsylvania, July 1–3, 1863. On October 25, 1863, Lieutenant Moylan was dismissed from the service for being AWOL (absent without leave) in Washington, D.C. He then enlisted under the assumed name of Charles Thomas into the 4th Massachusetts Volunteer Cavalry Regiment on December 2, 1863. Moylan was appointed a sergeant in that regiment on December 26, 1863, a first lieutenant, then a captain on December 1, 1864. He was then brevetted to the rank of major on April 9, 1865, and mustered out in November, 1865.