Goldsborough was given command of the Atlantic Blockading Squadron in September 1861, relieving Flag Officer Silas H. Stringham. In October of that year the Atlantic squadron was split into the North Atlantic Blockading Squadron and South Atlantic Blockading Squadron; Goldsborough took command of the North squadron, and Flag Officer Samuel Francis DuPont assumed command of the South squadron. On January 3, 1862, both officers were promoted to the newly created rank of Flag Officer (equivalent to the rank of Commodore which would be created 5 months later). During his command of the North Atlantic Blockading Squadron, which he commanded from its inception to September 1862, he led his fleet off North Carolina, where in cooperation with troops under General Ambrose Burnside, he captured Roanoke Island and destroyed a small Confederate fleet.