The Fort Yuma Indian School was located on the site of a former Civil War fort, which was tranferred to the Quechan Indian Tribe and the Department of the Interior in 1884. It was operated by the Sisters of St. Joseph of Carondelet on behalf of the United States government from 1886 to 1900. Control of the school was officially tranferred from the Department of the Interior to the Sisters of St. Joseph on April 5, 1886, and the sisters began holding classes in the fall of 1886. The first superintendent of the school was Sister Ambrosia (Mary O'Neil). The chief of the Yuma (Quechan) at the time, Chief Pascual, converted to Catholicism and encouraged Quechan children to attend the school. Chief Pascual died during a measles and chicken pox epidemic on May 5, 1887. He was succeeded by Chief Miguel, who opposed the school's mission and refused to compel tribe members to send their children to the school. At the Sisters' urging, Father J.A. Stephan of the Bureau of Catholic Indian Missions threatened Chief Miguel with the removal of Yuma children to Washington. After several years of increasing conflict, in 1893 government officials acting on behalf of the school forced the Quechan to select a new chief, Joe Palma, who was the son of Chief Pascual and whom they expected to view the school more favorably. In 1899, Patrick Miguel, the son of Chief Miguel, led a group of Quechan who attempted to set fire to the school. The Sisters of St. Joseph ultimately closed the school at the end of the 1900 term.
While the Sisters were nominally given control of the school, they and the United States government maintained a close relationship; school officials and government agents often cooperated. Throughout the 1890s, the school was involved in forcing Quechan farmers to sign leases through a government administered program and moving control over agricultural endeavors away from the tribe.
Patrick Miguel later gave testimony before a Senate commission in 1928, and emphasized "the inadequacy of the food provided to Quechan children."