During the Mexican–American War, he served in the brig Washington in the squadron of Commodore Matthew Perry, and took part in the capture of Tabasco, Mexico, on January 14–16, 1847.

President Abraham Lincoln gave him a temporary appointment in the Navy and sent him in the steamer Baltic to the relief of Fort Sumter.

On August 1, 1861, Lincoln appointed him Assistant Secretary of the Navy, an office which he held until the close of the Civil War.

In 1882 he published a paper suggesting that Samana Cay in the Bahamas was Guanahani, or San Salvador, the first island Christopher Columbus reached in his discovery of the Americas.

Fox is one of the primary viewpoint characters in novelist Harry Harrison's alternate history Stars and Stripes trilogy.