The first Hillsborough school was housed in the George Howard home located near Roehamptom and Richmond Roads. In 1911, it was used as a combination City Hall, Fire Department, and community center. A classroom was built, and a teacher-principal was hired for the six students enrolled.

The first portion of the SOUTH HILLSBOROUGH SCHOOL was completed in 1917. The school consisted of an office, cafeteria, library, and nine classrooms for children attending kindergarten through eighth grade. In 1930, the auditorium was built. During the 1940s, a section of the polo field was acquired for the playground, and in 1948, a field house was constructed. New classrooms and the Koshland Memorial Library were added in 1964. South has been designated a California Distinguished School in 1987, 1993, 1997, 2000, 2004 and 2008. 

NORTH HILLSBOROUGH SCHOOL opened its doors in September, 1950, with an enrollment of 175 children. Additions were completed in 1952 and 1956. In response to declining enrollment and limited state funding, North School was closed between 1985 and 1990. In the interim, it was used for recreational, educational and civic purposes. North has been designated a California Distinguished School in 1995, 2000, 2004 and 2010.

Land for the WEST HILLSBOROUGH SCHOOL was purchased in 1953, and the third elementary school was opened the following year. Additional facilities were built in 1955. The multi-media center was completed in 1972. West has been designated a California Distinguished School in 1987, 1993, 1997, 2000, 2004 and 2008.

In 1959, WILLIAM H. CROCKER MIDDLE SCHOOL was opened for seventh and eighth graders. The sixth graders became part of the student body in 1972. That same year, the Gertrude Hinton Learning Center, science facilities, gymnasium, and unified arts center were built. Crocker was designated a California Distinguished School in 1982, 1988, 1992, 1994, 1999, 2003 and 2007. Crocker also received the National Blue Ribbon Secondary School, Excellence in Education Award in 1983, 1989, 1996 and 2005. Crocker is the only middle school in the United States to be recognized four times. In 1993, Crocker achieved world class status by being recognized by the Royal Swedish Academy as one of the top five schools in the world.