Joining the navy as a midshipman, Stockton saw action in the War of 1812 and in the war against the Barbary pirates (1815). At home, he was active (1828–38) in the American Colonization Society, for which he had journeyed to Africa in 1821 to obtain the land that later became Liberia. In 1838 he went to sea again as commander of the flagship of the Mediterranean fleet. With the naval designer John Ericsson, he drew up the plans for the Princeton, the first warship to be driven with a screw propeller.

Late in 1845 he was chosen to command the Congress on its voyage from Norfolk, Va., to the Pacific Coast, where he had been ordered to take charge of the fleet. When war with Mexico erupted while he was en route, Stockton immediately took command of U.S. land and sea forces and proceeded to capture Los Angeles—a Mexican stronghold—on Aug. 13, 1846. Four days later, he set up a civil government and formally annexed California to the United States, first naming himself, and later the soldier-explorer John C. Frémont, as governor. In September, however, the two men again had to fight to subdue rebellious native Mexicans; this time they were assisted by Colonel Stephen Watts Kearny of the U.S. Army. The entire province was then ceded to the United States.

After resigning from the navy (1850), Stockton returned to New Jersey. He served as a U.S. senator (1851–53) and finally as president of the Delaware and Raritan Canal Company, which he had helped to form some 20 years earlier.