In 1888, Bishop Francis Mora of the Diocese of Monterey-Los Angeles Diocese, announced plans to build a school for Native American children in the area of the San Gorgonion Pass. It was part of a nationwide effort using both government and church run schools.
The cemetery opened sooner than expected when the school's first superintendent, Very Rev. George Willard died unexpectedly on July 26, 1890; this was less than five weeks before the scheduled opening of the school. In 1892, two students and one of the religious sisters who staffed the school died. From 1890 to 1941, there were 77 burials. Of the 77 interments, 24 were connected to the school. There were three priests, five religious sisters and 16 students. The remaining burials were of residents of Banning, Beaumont and the Morongo reservation.
After World War II, the cemetery began to deteriorate. This was due to changes with the school. In 1969, the trade school portion moved to Beaumont and the St. Boniface buildings were demolished in 1974. Also in 1974, the remains of the five sisters were exhumed and re-interred at Calvary Cemetery in Los Angeles.
On May 11, 1977, the County of Riverside designated the school and cemetery site as Historical Site No. 049. Through the years, different church and community groups have worked to maintain the cemetery property.