The fort was named after US Captain Samuel F. DuPont with the United States Navy that arrived on July 29, 1846, aboard USS Cyane with Major John C. Frémont and his troops, also Kit Carson and his men.

The fort was abandoned shortly to Mexican Californios, Francisco Rico, and Serbulo Varela with 50 of his troops.

Mexican Ramon Carrillo and Captain Leonardo Cota returned with troops to retake the fort on October 26, 1846.

Mexicans Santiago Arguello and Miguel de Pedrorena joined the US forces to retake the fort.

At the end of the short war with the Treaty of Guadalupe Hidalgo on February 2, 1848, Fort Stockton was abandoned on September 25, 1848.