On November 1, 1871, he was elected as a Companion of the New York Commandery of the Military Order of the Loyal Legion of the United States – a military society of officers who had served the Union during the American Civil War. He was assigned insignia number 1338.
Between 1873 and 1875 he commanded the Juniata on its cruise to Greenland in search of the ill-fated Polaris Expedition. During this cruise, he was promoted to the rank of captain in 1874. In 1875, he took command of the receiving ship USS Colorado, after which he was assigned to command USS Powhatan. As a senior captain, Braine was permitted to use the customary title commodore beginning in 1885, and in late 1886 he was assigned to command the South Atlantic Squadron with promotion to rear admiral the following year. In 1889 he was assigned to command of the Brooklyn Navy Yard, where he served until his retirement.
Retirement and death
Rear Admiral Braine retired from the Navy in May 1891.
In 1895 he became a Veteran Companion of the New York Commandery of the Military Order of Foreign Wars and received insignia number 45.