In addition to service in the northeastern United States from then through 1928, S-13 operated in the Panama Canal area from February through April 1926; visited Kingston, Jamaica, from 20 to 28 March 1927, and served again in the Panama Canal area from February to April 1928. From 1929 to 1936, she operated almost exclusively in the Panama Canal area, although she visited Baltimore, Maryland, from 15 May to 5 June 1933, and New London from 15 May to 1 June 1935. Departing Coco Solo in the Panama Canal Zone on 13 June 1936, she was decommissioned on 30 September 1936 at Philadelphia, Pennsylvania.
1940–1945
S-13 was recommissioned on 28 October 1940. Following voyages to Bermuda, S-13 operated in the Panama Canal area from December 1941 (during which the United States entered World War II with the Japanese attack on Pearl Harbor on 7 December) to June 1942; off Guantanamo Bay, Cuba, from June to August 1942; and in the Panama Canal area beginning in August 1942. She was patrolling on the surface in the Gulf of Panama off Balboa, Panama, at the Pacific entrance to the Panama Canal at 07°32′N090°50′W / 7.533°N 90.833°W / 7.533; -90.833 on 3 August 1942 when a four-engine United States Army Air Forcesbomber approached her and mistakenly attacked her, dropping a number of bombs into the water near her, one of which exploded.[1] She then exchanged recognition signals with the bomber, which departed without further incident.[1] She suffered no casualties or damage.
S-13 operated in the Panama Canal area until January 1944, then at Trinidad from February 1944 to May 1944. at Guantanamo Bay from May through July 1944. and in the Panama Canal area through the remainder of 1944. Departing Coco Solo on 3 January 1945, S-13 proceeded to Philadelphia for inactivation.