San Juan Capistrano is served by Capistrano Unified School District.
In the 2007–08 academic year, San Juan Hills High School opened with about 600 freshman students.
It is the city's only public high school.
Ultimately, nearly all San Juan Capistrano's high school students will move to this campus as well as some students from Capistrano Beach, San Clemente High School, and southern Ladera Ranch.
Residents from these other communities did not want to attend a school in San Juan on the pretense that these communities had too many differences, a perspective fueled by anti-Hispanic sentiment in the whiter, more affluent communities.
Many residents wanted to stay at the established high schools their communities had been attending for years.
While there was initially tension caused by the boundary changes implemented with the construction of the new high school, it has since died down.
The main relief for the tension was the construction of a connecting road from Avenida La Pata to Avenue Vista Hermosa, allowing for students from San Clemente to take a more direct route to the school.
The $127 million infrastructure project completed on August 13, 2016.

San Juan has four public elementary schools (grades K–5): Del Obispo Elementary School, Harold Ambuehl Elementary School, Kinoshita Elementary School, and San Juan Elementary School.
The local public middle school (grades 6–8) is Marco Forster Middle School.
Capistrano Valley High School (grades 9–12) lies just outside of the city's borders, but serves many of the city's students.

A public continuation high school, Junipero Serra High School, also serves the area.
Not to be confused with the Catholic school to the north, the Serra High School is a campus dedicated to helping adults finish their pre-collegiate educational goals.

San Juan also has six private, non-secular schools.
Capistrano Valley Christian Schools (grades pre-K – 12), Saddleback Valley Christian School (grades pre-K – 12), St. Margaret's Episcopal School (grades pre-K – 12), and JSerra Catholic High School (grades 9–12).
Mission Basilica School (grades K–8) is located on the historic Mission grounds, utilizes some of the historic buildings as classrooms, and is part of Mission Basilica San Juan Capistrano.
The other is Rancho Capistrano Christian School (grades K–8), located off Interstate 5 on Saddleback Church's south campus.
San Juan Capistrano is served by Capistrano Unified School District. In the 2007–08 academic year, San Juan Hills High School opened with about 600 freshman students. It is the city's only public high school. Ultimately, nearly all San Juan Capistrano's high school students will move to this campus as well as some students from Capistrano Beach, San Clemente High School, and southern Ladera Ranch. Residents from these other communities did not want to attend a school in San Juan on the pretense that these communities had too many differences, a perspective fueled by anti-Hispanic sentiment in the whiter, more affluent communities. Many residents wanted to stay at the established high schools their communities had been attending for years. While there was initially tension caused by the boundary changes implemented with the construction of the new high school, it has since died down. The main relief for the tension was the construction of a connecting road from Avenida La Pata to Avenue Vista Hermosa, allowing for students from San Clemente to take a more direct route to the school. The $127 million infrastructure project completed on August 13, 2016.
San Juan has four public elementary schools (grades K–5): Del Obispo Elementary School, Harold Ambuehl Elementary School, Kinoshita Elementary School, and San Juan Elementary School. The local public middle school (grades 6–8) is Marco Forster Middle School. Capistrano Valley High School (grades 9–12) lies just outside of the city's borders, but serves many of the city's students.
A public continuation high school, Junipero Serra High School, also serves the area. Not to be confused with the Catholic school to the north, the Serra High School is a campus dedicated to helping adults finish their pre-collegiate educational goals.
San Juan also has six private, non-secular schools. Capistrano Valley Christian Schools (grades pre-K – 12), Saddleback Valley Christian School (grades pre-K – 12), St. Margaret's Episcopal School (grades pre-K – 12), and JSerra Catholic High School (grades 9–12). Mission Basilica School (grades K–8) is located on the historic Mission grounds, utilizes some of the historic buildings as classrooms, and is part of Mission Basilica San Juan Capistrano. The other is Rancho Capistrano Christian School (grades K–8), located off Interstate 5 on Saddleback Church's south campus.
San Juan Capistrano, California