James Wallace Cooke was born in Beaufort, North Carolina, and was orphaned at the age of 4.

At the start of the Civil War in 1861 Cooke joined the Virginia State Navy, and entered the service of the Confederacy in the following June.

Later that year he was placed in command of the small gunboat CSS Ellis, and was captured with her after a hard fight near Roanoke Island, North Carolina on February 10, 1862.

That June he was promoted to the rank of captain and was later placed in charge of Confederate naval forces on North Carolina's internal waters, holding that position until the end of the Civil War in 1865.

James W. Cooke died at Portsmouth, Virginia in 1869, and is buried at Cedar Grove Cemetery.