Carson played a prominent and memorable role in the Civil War in New Mexico. He helped organize the New Mexico volunteer infantry, which saw action at Valverde in 1862. Most of his military actions, however, were directed against the Navajo Indians, many of whom had refused to be confined upon a distant reservation set up by the government. Beginning in 1863 Carson waged a brutal economic war against the Navajo, marching through the heart of their territory to destroy their crops, orchards and livestock. When Utes, Pueblos, Hopis and Zunis, who for centuries had been prey to Navajo raiders, took advantage of their traditional enemy's weakness by following the Americans onto the warpath, the Navajo were unable to defend themselves. In 1864 most surrendered to Carson, who forced nearly 8,000 Navajo men, women and children to take what came to be called the "Long Walk" of 300 miles from Arizona to Fort Sumner, New Mexico, where they remained in disease-ridden confinement until 1868.

After the Civil War, Carson moved to Colorado in the hope of expanding his ranching business. He died there in 1868, and the following year his remains were moved to a small cemetery near his old home in Taos.