Born in Dublin, Ireland, Rowan came to the United States at the age of 10 and lived in Piqua, Ohio. Rowan was a graduate of Miami University and was appointed as a midshipman in the U.S. Navy on 1 February 1826 at the age of 17. Later, he took an active role in the Mexican–American War, serving as executive officer of the sloop during the capture of Monterey, California on 7 July 1846, and in the occupation of both San Diego and Los Angeles. In January 1847 he led a provisional battalion, with the nominal rank of major, of seven companies of naval infantry for the recapture of Los Angeles.
Civil War service
Captain of the steam sloop at the outbreak of the American Civil War, he attempted to relieve Fort Sumter and to burn the Norfolk Navy Yard. In the fall of 1861, he assisted in the capture of the forts at Hatteras Inlet; then, taking command of a flotilla in the North Carolina sounds, he cooperated in the capture of Roanoke Island in February 1862. Promoted simultaneously to captain and commodore for gallantry, he then supported the capture of Elizabeth City, Edenton, and New Bern. During the summer of 1863, he commanded the broadside ironclad on blockade duty off Charleston, South Carolina and the following August assumed command of Federal forces in the North Carolina sounds. During this time the rebel semi-submersible CSS Davidattacked the New Ironsides with a spar torpedo. In the ensuing explosion, one man was killed and a large hole was torn into the ironclad but she continued her blockading duties.
Post Civil War service
Commissioned rear admiral on 25 July 1866, Rowan served as Commandant of the Norfolk Navy Yard until 1867, when he assumed command of the Asiatic Squadron. Returning in 1870, he was appointed vice admiral, following the death of Admiral David Farragut and the promotion of Vice Admiral David Dixon Porter in August of that year. In December 1870 Rowan reached the mandatory retirement age of 62 but, like admirals Farragut and Porter before him, he was allowed to remain on active duty. Rowan served as Commandant of the New York Navy Yard from 1872 to 1876, as Governor of the Naval Asylum at Philadelphia, Pennsylvania in 1881, and as Superintendent of the Naval Observatory, Washington, D.C., from 1882 until his retirement in 1889. Rowan had a 63-year career, which was one of the longest in the history of the United States Navy. In 1882 Admiral Rowan was elected as a First Class Companion of the District of Columbia Commander of the Military Order of the Loyal Legion of the United States. He was assigned MOLLUS insignia number 2510. Rowan's son, Hamilton Rowan, an officer in the U.S. Army, was elected as a Second Class Companion of MOLLUS and became a First Class Companion upon his father's death. Rowan died in Washington, D.C. on 31 March 1890 at the age of 81.