During the American Civil War, Army reorganization created the Department of the Pacific on January 15, 1861. On December 12, 1861, the District of Humboldt was created, consisting of the counties of Sonoma, Napa, Mendocino, Trinity, Humboldt, Klamath, and Del Norte in Northern California. The district was headquartered at Fort Humboldt, located on a bluff above the central portion of Humboldt Bay south of Eureka, California, which is now a California State Historic Park located within the City of Eureka. The District's efforts were directed at prosecuting the ongoing Bald Hills War against the Indians in the northern, coastal area of the large district. A peace was achieved in August 1864.
On July 27, 1865, the Military Division of the Pacific was created, consisting of the Department of California and Department of the Columbia. Humboldt District was absorbed by the Department of California.