After leaving the North Pacific Squadron, Rodgers performed ordnance duty at the Washington Navy Yard in Washington, D.C., in 1872. He was the first commanding officer of the newly acquired steamer from 1873 to 1876, during which time the ship was engaged in special service. He was promoted to commander on 4 February 1875. After duty as a lighthouse inspector on the Great Lakes from 1876 to 1877, Rodgers was the commanding officer of the screw gunboat in the South Atlantic Squadron and later in the Pacific Squadron from 1878 to 1879. He then served a second tour as a lighthouse inspector, this time at Philadelphia, Pennsylvania, from 1881 to 1883 before a tour from 1883 to 1886 as commanding officer of the receiving ship at Mare Island Navy Yard in Vallejo, California. He was a lighthouse inspector again from 1888 to September 1890, in charge of the Lighthouse Depot, and was promoted to captain on 26 or 28 February 1890 (sources vary). Rodgers returned to sea as commanding officer of the protected cruiser from September 1890 to July 1892, then served as Supervisor of the Harbor of New York from July 1892 to September 1893. His next tour was as Captain of the Yard at the New York Navy Yard in Brooklyn, New York, from 1893 to 1896. He took command of the new battleship as her first commanding officer when she was commissioned on 10 June 1896. During the Spanish–American War he commanded the coastal monitor which operated in both the Cuban and Puerto Rican Campaigns. Following the war, he served as President of the Board of Inspection and Survey from 1 December 1898 until 1901, being promoted to commodore on 25 September or 25 December 1898 (sources vary) and to rear admiral on 3 March 1899. In May 1901, Rodgers became Senior Squadron Commander within the Asiatic Squadron, and, on 1 March 1902, he became the commander of the entire Asiatic Squadron, which was engaged in combat during the Philippine–American War at the time. He was the squadrons last commander, as at the end of his tour on 29 October 1902 the Asiatic Squadron was abolished and its responsibilities were assumed by the new United States Asiatic Fleet. While in the Asiatic Squadron, Rodgers was at the center of a legal case, "Frederick Rodgers v. United States", involving a claim Rodgers made for additional pay he believed was due him and eight other rear admirals in the wake of the passage by the United States Congress of the Navy Personnel Act of 3 March 1899.