In 1938, the U.S. government took over the management of the Dollar Steamship Co. which was in financial difficulties and transferred their assets to the newly formed American President Lines.By 1940, the U.S. government had commissioned 16 new ships for APL, continuing the "president" naming of ships, one of these examples being SS President Jackson, a C-3 class merchant vessel. In 1941, the US entered World War II, and in 1942 the War Shipping Administration was created. APL worked on the management of some of the Administration's ships, maintaining and overhauling them as well as crewing them and being responsible for the handling of cargo and passengers.

In the 1950s, the company again expanded, building more ships; 11 were built between 1952 and 1954. by later 50's the company invest in containerization.