Joining the Navy in 1840, he was graduated from the Naval Academy in 1846 and promoted lieutenant in 1855. In 1861, following the expedition to relieve Fort Sumter, he participated in secretly surveying and buoying Confederate coastal waters and inlets, occasionally engaging enemy vessels and shore batteries, before commanding screw sloop Juniata under RAdm. David Dixon Porter in the 1965 attack on Fort Fisher, Wilmington, North Carolina.
Promoted captain in 1871, commodore in 1879 and rear-admiral in 1884, he retired in 1885 and died at New York City 10 January 1901.
His son, Thomas Stowell Phelps, Jr., also attained the rank of rear admiral.
