He was born in Corsica, Pennsylvania, to John Jamison Thompson and Agnes Kennedy. He was appointed to the United States Naval Academy on 30 July 1864. Graduating tenth in the class of 1868, Thompson first went to sea in Contoocook in the West Indian Squadron. He later served in Franklin, Richmond, and Guard of the Mediterranean Squadron; as well as in Wachusett and at the Naval Torpedo Station, Newport, Rhode Island.