At the start of the American Civil War he volunteered for service. He was given a temporary appointment in the Navy and was sent in the steamer Baltic to the relief of Major Robert Anderson and the remnant of his command in Fort Sumter, and brought them away.
On 1 August 1861, President Abraham Lincoln appointed him Assistant Secretary of the Navy, an office which he held until the close of the Civil War. In 1866, he was sent on a special mission to Russia and conveyed the congratulations of the President of the United States to Tzar Alexander II upon his escape from assassination. His voyage was made in the monitor Miantonomoh which was the first vessel of this class to cross the Atlantic. They were accompanied by Augusta.
In 1882 he made a publication suggesting Samana Cay in the Bahamas to be Guanahani, or San Salvador, the first island Christopher Columbus reached at his discovery of the Americas. Little attention was paid to it until 1986, when the National Geographic Society also appointed Samana Cay to be San Salvador.
He died at Lowell, Massachusetts, aged 62.
Two ships have been named USS Fox in his memory.