Warranted a passed midshipman in June 1852, Breese took part in Commodore Matthew C. Perry's expedition to Japan for the next three years.

Lieutenant Breese's next duties were as an officer of the sloop of war Portsmouth, off Africa, in 1860, and of the steamer San Jacinto from mid-1860 until late 1861.

Promoted to lieutenant commander in mid-1862, he served with Rear Admiral David Dixon Porter on the Mississippi River and off the United States East Coast for most of the rest of the conflict, distinguishing himself during the Siege of Vicksburg, commanding 2,000 sailors and Marines in the successful land assault on Fort Fisher, and as Porter's Fleet Captain.

Beginning in September 1865, Breese spent a year as Assistant to the Naval Academy's Superintendent, achieving the rank of commander while in that post.

He was Commanding Officer of the steam sloop Pensacola, the Pacific Squadron flagship, in 1879 and 1880 and, in 1881, was a member of the Board of Harbor Commissioners.