While conducting submerged trials in Long Island Sound on 5 October 1918, prior to her commissioning, O-13 rammed USS Mary Alice, the section patrol boat accompanying her, during a submerged circular run off Bridgeport, Connecticut, holing Mary Alice amidships.

O-13 operated along the coast of New Jersey and New York until 8 October 1919, when she arrived Philadelphia Navy Yard for a five-month overhaul.

After returning to Cape May, New Jersey, on 8 March 1920, she departed on 1 April for duty in the Caribbean Sea.

Steaming via Key West, Florida, and Havana, Cuba, she arrived Coco Solo, Panama Canal Zone, on 30 April.

For over three years O-13 operated out of the Submarine Base at Coco Solo both in the Caribbean Sea and in the Pacific Ocean.