During the 45 years he served in the U.S. Navy, Buchanan had extensive and worldwide sea duty.

He commanded the sloops of war Vincennes and Germantown during the 1840s and the steam frigate Susquehanna in the Perry Expedition to Japan from 1852 to 1854.

With the Civil War upon him, he resigned his commission on April 22, 1861, expecting his home state of Maryland to eventually secede.

On September 5, 1861, Franklin Buchanan joined the Confederate Navy and was given a captain's commission.

On February 24, 1862, the Confederate States Secretary of the Navy, Stephen Mallory, appointed Buchanan to the office of Confederate Navy James River Squadron Flag Officer and he then selected the newly built ironclad CSS Virginia to be his flagship.

[2] He climbed to the top deck of Virginia and began furiously firing toward shore with a carbine as USS Congress was shelled.

He was on board Tennessee during the Battle of Mobile Bay with Rear Admiral David Glasgow Farragut's Union fleet on August 5, 1864.