In the 1840s, he was hired as a guide by John C. Fremont. Fremont's expedition covered much of California, Oregon, and the Great Basin area. Fremont mapped and wrote reports and commentaries on the Oregon Trail to assist and encourage westward-bound American pioneers. Carson achieved national fame through Fremont's accounts of his expeditions.

Under Fremont's command, Carson participated in the uprising against Mexican rule in California at the beginning of the Mexican-American War. Later in the war, Carson was a scout and courier, celebrated for his rescue mission after the Battle of San Pasqual and for his coast-to-coast journey from California to Washington, DC to deliver news of the conflict in California to the U.S. government. In the 1850s, he was appointed as the Indian agent to the Ute Indians and the Jicarilla Apaches.

During the American Civil War, Carson led a regiment of mostly Hispanic volunteers from New Mexico on the side of the Union at the Battle of Valverde in 1862. When the Confederate threat to New Mexico was eliminated, Carson led forces to suppress the Navajo, Mescalero Apache, and the Kiowa and Comanche Indians.

Carson was breveted a Brigadier General and took command of Fort Garland, Colorado. He was there only briefly: poor health forced him to retire from military life. Carson was married three times and had ten children. The Carson home was in Taos, New Mexico. Carson died at Fort Lyon, Colorado, of an aortic aneurysm on May 23, 1868. He is buried in Taos, New Mexico, next to his third wife Josefa Jaramillo.