After the war, he commanded the coastal survey ship Hassler from 1871 to 1872 during an expedition to the Strait of Magellan and both southern coasts of South America accompanied by natural historian Louis Agassiz.

[1][2] After the outbreak of the Civil War, Johnson was given command of the captured steamer USS Tennessee in the Western Gulf Squadron until 1863.

[4][5] From April 1864 to February 1866, Johnson was assigned to the Naval Academy and given command of the training ship USS Constitution, first at Newport, Rhode Island and then returning to Annapolis, Maryland after the end of the Civil War.

He was promoted to captain on 14 June 1874 and given command of the screw sloop USS Omaha in the South Pacific Squadron.

From November 1881 to June 1884, he was assigned as Chief Signal Officer at the Navy Department in Washington, D.C.[4] On 28 July 1884, Johnson was promoted to commodore.

[4] Selected to command the Pacific Squadron, Johnson died in Portsmouth, New Hampshire on the morning of 28 January 1887, only a few hours before his scheduled promotion to rear admiral.

His father was a businessman who was appointed Secretary of State of Maine by Governor John Fairfield and then served in the civilian leadership of the Navy Department during the Polk administration.

[12] Naval officer Alfred Wilkinson Johnson, who retired from active duty as a vice admiral, was their son.