He was attached first to the bomb brig USS Stromboli in the Home Squadron from 1847 to 1848, seeing service on blockade duty off Mexico during the Mexican War.

He attended the United States Naval Academy in Annapolis, Maryland, from 1853 to 1854 and, upon completing his studies, was promoted to passed midshipman on 15 June 1854.

[2][3] Fyffe was assigned to special service aboard the screw frigate USS San Jacinto in 1855, and was promoted to lieutenant on 16 September 1855.

He served aboard the steam frigate USS Minnesota, flagship of the North Atlantic Blockading Squadron, from 1863 to 1865.

[2][4] After the Civil War, Fyffe performed duty at the Boston Navy Yard in Charlestown, Massachusetts, in 1867 and was promoted to commander on 2 December 1867.

En route X on foot X requested recruiting officer be authorized issue me new shoes X shoes fell apart noon today X entered Albany (New York) barefooted X will remain Seward Hotel two days awaiting answer X earned my keep as bartender X local rum far superior to that served in the US Navy X am sending sample X very respectfully Fyffe."

"Pass following message to Lt. Comdr J. P. Fyffe USN now at Seward Hotel Bar Quote I strike my colors X United States Secretary of the Navy authorizes recruiting officer Albany issue you shoes and provide you quickest transportation from Albany to San Francisco X Even Chief Bureau of Navigation (United States Navy) can laugh when outsmarted X unquote X Respectfully Bureau of Navigation".