In 1859, Rodgers was appointed Commandant of Midshipmen at the Naval Academy, serving there until the start of the Civil War in 1861, in which he saw action at the Battle of Port Royal and the Siege of Fort Pulaski. After the war, he served as Chief of the Bureau of Yards and Docks from 1871 to 1874 and later as Superintendent of the Naval Academy until 1878, before a two-year tour as Commander of the Pacific Squadron and returning to the Naval Academy as superintendent in 1881, retiring in November of that year.

This picture of Rodgers was taken sometime between 1860 and 1865, during the Civil War, and is in the collection of the Library of Congress in Washington, D.C.