The Foundation was originally created as the Sakya Foundation in June of 1998, with Her Eminence Jetsun Kushok as the Chair. It was created to hold a parcel of land in the Napa Valley, donated to Her Eminence, with the intent that the proceeds of the land sale be used towards the building of a monastery or other charitable purposes. The Sakya Foundation received its determination letter from the Internal Revenue Service, granting it IRC 501(c)(3) tax-exempt status in May 1999. In 2015, H. E. Jetsun Kushok decided to retire and requested His Holiness the 42nd Sakya Trizin Rinpoche to head the Sakya Foundation.

His Holiness the 42nd Sakya Trizin bestowed a new name, the “Sachen Foundation,” and the name was officially changed with the Internal Revenue Service in 2017. A determination letter from the Internal Revenue Service, recognizing the Sachen Foundation’s IRC 501(c)(3) tax-exempt status, was issued in December 2017.