Most tribes and nations of Native Americans did not have amiable relations with the government of the United States. A long history of broken promises and violated treaties meant that thousands of Indians had been pushed off their land and forced to settle further west, or on reservations. During the Civil War, many remained tribes tried to remain neutral. Nevertheless, their loyalty to the Union was often severely tested. Because the war absorbed so many government resources, the annuities owed to the Santee Sioux in Minnesota were not paid on time in the summer of 1862. In addition, Long Trader Sibley refused the Santee Sioux access to food until the funds were delivered. In frustration, the Santee Sioux, led by Little Crow (Ta-oya-te-duta), attacked settlers. After the Sioux lost the fighting, they were tried (without defense lawyers), found guilty on flimsy evidence. After 303 Santees were sentenced to death, and 16 sentenced to long prison terms, President Lincoln was presented with the situation. According to General John Pope, commander of the Military Department of the Northwest, "the Sioux prisoners will be executed unless the President forbids it, which I am sure he will not do."

Lincoln requested full information about the convictions, and assigned two attorneys to examine the cases and differentiate between those guilty of murder and those simply engaged in battle. General Pope, as well as Long Trader Sibley, whose refusal to allow the Indians access to food had been largely responsible for the war, were angered by Lincoln's failure to immediately authorize the executions. They threatened that the local settlers would take action against the Sioux unless the President allowed the executions quickly. In addition, they arrested the rest of the Santee Sioux, 1,700 people, of whom most were women and children, although they were accused of no crime. On December 6, 1861, Lincoln authorized the execution of 39 Sioux, and ordered that the others be held pending further orders, "taking care that they neither escape nor are subjected to any unlawful violence." On December 26, 39 men were taken. At the last minute, one was given a reprieve, but it would not be publicized until years later that 2 of the men hanged were not authorized by Lincoln. In fact, one of these two men had saved a white woman's life during the fighting. Little Crow was killed in July of 1863, the year in which the Santees were transported to a reservation in Dakota Territory.

Other Native American tribes, including the Cheyennes and the Arapaho, engaged in serious clashes with Union troops. Some of these conflicts were ignited when Union troops, scouting for Confederates, met Native Americans on hunting trips, or raided Indian settlements.

Although there was a war going on, settlers did not stop pressuring the United States government to push Native Americans off their land to facilitated western expansion. In October of 1862, Brig. Gen. James H. Carleton commanded Col. Christopher "Kit" Carson and five companies in the Department of New Mexico to begin operations against Mescalero Apache and Navajo Indians in the District of Arizona. The Native Americans were to be captured and confined in the Bosque Redondo Reservation in the eastern part of the New Mexico Territory. Anyone who resisted was to be killed.

While the Mescalero Indians either escaped to Mexico or were removed to the reservation, the Navajos provided more resistance to the federal removal attempt. Navajos tried to negotiate a peace agreement, but were rejected in their efforts. At that point, they began a struggle for the right to keep their land. The federal troops adopted a "scorched-earth policy," by which they destroyed Navaho farmland and forced the Navajos to the point of starvation. The Indians surrendered as individuals or in small groups, while those who fled were pushed to the Canyon de Chelly in what would become Arizona. Col. Carson led troops to the Canyon de Chelly, killing and capturing some Navajos, and forcing the surrender of 200 people. Eventually, 11,468 Navajos were held at Fort Canby, and marched to the Bosque Redondo Reservation, which 425 miles away. This cruel march is called 'The Long Walk," and is estimated to have caused the death of about 3,000 Navajos from starvation and/or abuse. Within two years of confinement in the reservation, another 2,000 Navajos died.

While Union forces tended to alienate Native Americans, the Confederate leadership expressed an interest in making alliances with the Indians in the Indian Territory. Confederate officer Albert Pike, who had made many contacts among Native American tribal leaders, and had helped the Creeks and other tribes obtain $800,000 in a long court battle with the federal government, was a clear choice for a Confederate envoy to the Native Americans. He was able to convince many Indian leaders to support the Confederacy. On October 7, 1861, he negotiated a treaty with the Chief John Ross of the Cherokee Nation, which provided more generous terms than the treaties with the United States for members of the "Five Civilized Tribes": Cherokee, Creek, Choctaw, Chickasaw and Seminole. As a brigadier general, Pike began training three Confederate regiments of Native Americans. Pike's troops fought victoriously at the Battle of Pea Ridge, but were routed by a Union counterattack. Unable to reassemble his troops, he contributed to the Confederate defeat. Later, the Union claimed that the Native Americans had scalped some of the dead or wounded soldiers on the field.

After the Battle of Pea Ridge, the service of Indian troops was restricted to fighting in Indian Territory. Nevertheless, many Native Americans served as scouts for the Confederacy; and one, Stand Watie, obtained the rank of general in the Confederate Army. Elias Cornelius Boudinot (1835-1890), a prominent Cherokee lawyer, represented the Cherokee Nation at the first and Second Confederate Congresses. Although he helped promote measures to provide food and supplies for Indian refugees, he was apparently involved in rather shady deals, some of which violated Cherokee-Confederate treaties. After the Confederates were defeated, however, Boudinot helped negotiate a peace between the United States and the Cherokee nation.

Neither the Confederacy nor the Indian troops ultimately benefited from their alliances. The Confederacy gained little military advantage from the help of Native Americans, except for the service of scouts. In fact, Confederate warfare was denigrated in the North when the traditional acts of Indian warfare, including scalping, were publicized in the Northern press as indications of Confederate depravity. Native Americans hardly fared better. Confederate coffers being so low, little food or other aid could be provided for Indians struggling with the challenges of a wartime economy. In addition, after the Civil War ended, Native American tribes and nations that fought with the Confederacy had their treaties with the federal government nullified.