Atkinson transferred to the in September 1860 and served on that ship as a yeoman during the American Civil War. He was present at the Battle of the Head of Passes of the Mississippi River on October 12, 1861, and at an engagement against Fort McRee near Pensacola, Florida, in November 1861. In the April 1862 Battle of Forts Jackson and St. Philip, "Richmond" fought Confederate ships in the Mississippi and passed artillery batteries at Chalmette, Louisiana, leading to the capture of New Orleans. The ship then proceeded up the river and Atkinson participated in the passage of Vicksburg, Mississippi, in mid-1862 and the action at Port Hudson in March 1863. At the Battle of Mobile Bay on August 5, 1864, he was in charge of supplying ammunition to the ship's Parrott rifle. For his "coolness and energy" in this battle, he was awarded the Medal of Honor four months later, on December 31, 1864.