On March 27, 1881, at the invitation of Father William Gleeson, pastor of St. Anthony Church in Brooklyn, (East Oakland), Sister Marie de Sacre Coeur and the Sisters of Notre Dame de Namur founded an academy for girls, grades one through twelve, on a plot of land on the corner of Chestnut Street and San Jose Avenue in Alameda.

McNaboe requested the Sisters of Notre Dame de Namur to staff a boys elementary school.

In 1916 Father James Bernard Praught opened Saint Joseph Elementary School for the boys and girls of the parish.

Oakland Bishop John Stephen Cummins later invited the Congregation of the Sacred Hearts of Jesus and Mary.

Student demographics reflect the Bay Area's cultural and ethnic diversity: African-American 13%, Asian 11%, Euro-American 29%, Filipino 12%, Latino 16%, Native American 1%, Multiracial/Other 17.7%.

The school offers project-based learning and innovative courses including Coding, Mandarin, and a Biomedical Sciences program with STEM curricula.

Ninety-nine percent of the senior class of 2014 enrolled in college, and graduates were offered just under $6 million in scholarships and awards.

For more than three decades the school's arts magazine Prisms has showcased student visual and literary works as well as original musical scores, earning first-place awards and other honors from The American Scholastic Press Association and National Council of Teachers of English.

St. Joseph Notre Dame offers interscholastic sports teams in baseball, basketball, cheerleading, crew, cross country, golf, lacrosse, soccer, softball, swimming, tennis, track and field, and volleyball.

In 2004, SJND won the Boys' Division IV Championship against Verbum Dei High School of Los Angeles, 49–47.

[8] SJND also appeared in the 2009 Boys' Division V Finals, losing to Windward High School of Los Angeles, 69–53.

This includes: Cameron Ba ('18-UCD); Kevin Butler ('00-UCR); Hondre Brewer ('98-USF); Blandon Ferguson ('99-Illinois); Jon Gordon ('96-SMC); Alex Harris ('04-UCSB); Allen Hester ('05-Ohio); Renee Jacques ('98-CSUS); Brandon Keane ('11-N.CO); Adrian McCullough ('96-UNR); Nate Murase ('98-CSUS); Miles Tarver (UoM); David Victor ('93-UNR/CSUS); Julian Vaughns ('19-CSUS); Ari Warmerdam ('02-UCD); Temidayo Yussuf ('14-LBSU).

Pilots Rashawn Fulcher ('97) and Benjamin Ortner ('01) were also Division II National Champions for Metropolitan State of Denver.