Ammen entered the Navy as a midshipman on 7 July 1836 and following the basic training, he was attached to the newly commissioned supply ship USS Relief, which was preparing for the Wilkes Exploring Expedition to Antarctica.

Ammen commanded the ship in the Mediterranean during the crisis caused by First Schleswig War and returned to the United States with that vessel in November 1850.

[1] Following a tour of coast survey duty, Ammen was ordered to the gunboat USS Water Witch under command of Lieutenant Thomas J.

Ammen was transferred to the Flagship of the Pacific Squadron, USS Merrimack and served under Commodore John C. Long until ship's return to the United States in February 1860.

Ammen was appointed commanding officer of newly commissioned gunboat USS Seneca in September that year and took part in the South Atlantic Blockading Squadron.

[1] Ammen then participated in the Battle of Port Royal on November 7, 1861, and was commended for bravery, when he went ashore to hoist the flag over the surrendered forts, and hold them till the army took possession.

He then took part in the actions on the Wilmington River at the end of January 1862 and participated in the capture of several Confederate vessels and the town of Fernandina, Florida.

He then assumed temporary command of the USS Shenandoah in March that year and served with the North Atlantic Blockading Squadron for one month, before he was appointed officer-in-charge of Marine recruits aboard the merchant vessel SS Ocean Queen in May 1864.

[3][4] Captain Tinklepaugh, who had expected the difficulty and was prepared, aimed his revolver at the head of the one of mutineers' leaders, and warned him that if he advanced a step further he would lose his life.

[1] Following the War, Ammen was assigned to the Naval Machinery at Charlotte, North Carolina, in July 1865 and remained there until September that year, when he was appointed commanding officer of the monitor USS Miantonomoh.

[1] He was appointed commanding officer of a newly commissioned screw steamer USS Piscataqua at Portsmouth Navy Yard and served within the Asiatic Station until February 1869.

While in this assignment, his principal responsibilities were to provide nautical charts and instruments and to oversee several activities involved navigation research, including the Naval Observatory.

Afterwards he was a member of the board to locate the new Naval Observatory, and a representative of the United States at the Interoceanic Ship Canal Congress in Paris.

He designed a cask balsa to facilitate the landing of troops and field artillery, a life-raft for steamers, and the steel ram USS Katahdin in 1893.