The areas which now include Sequoyah Heights, Sequoyah Hills and Sequoyah Highlands, were once apart of the famous Rancho San Antonio, a large section of land that was granted to Luis Peralta, the last Spanish governor of California in 1820. This large section of land was later divided into three sections of land, one passing to Ygnacio Peralta, which today encompasses most of the Sequoyah communities today. The Sequoyah Hills currently has an active neighborhood association.

For much of the late 19th and early 20th centuries, the land sat vacant and untouched. Natural plant life and animals roamed free. It was not until the beginning of World War II , that eventually brought development to the area. The United States Navy found within the Sequoyah hills area a central place to locate a naval hospital. This Navy Hospital began in 1942 as a temporary hospital to handle battle casualties returning from the Pacific. At first it consisted of 25 wooden barracks built on the site of the Oak Knoll Golf Course. Expansions were made during and after the war and the hospital evolved into a modern regional hospital handling naval personnel needing specialized care from a 10,000 square mile area of California and Nevada. The influx of personnel brought growth to the area. The communities of the Sequoyah Hills began to expand and by the 1960s, many new tract developments has been established, bringing new families to the area. In the early 1990s, the base underwent downsizing and huge cuts in spending. The Naval Regional Medical Center, which it later became known in Oakland, was closed in 1996.