Haffee enlisted in the Navy in December 1862 and was assigned to the Union sloop-of-war United States Ship (1862). His enlistment is credited to the state of Maryland. On January 15, 1865, the North Carolina Confederate stronghold of Fort Fisher was taken by a combined Union storming party of sailors, marines, and soldiers under the command of Admiral David Dixon Porter and General Alfred Terry.
He received the Medal of Honor for his actions during the Second Battle of Fort Fisher on January 15, 1865. The President of the United States of America, in the name of Congress, takes pleasure in presenting the Medal of Honor to Quartermaster Joseph B. Hayden, United States Navy, for extraordinary heroism in action while serving on board the United States.S. TICONDEROGA, as Quartermaster in charge of steering the ship into action, during attacks on Fort Fisher, North Carolina, 13 to 15 January 1865.
