RESCU Academy was founded by Art Aragon and Cheryl Zak in 1996 as an after-school treatment program for students struggling with substance abuse and other mental health issues.  In 1999,RESCU Academy became a full-time school support program which students attended the program Monday through Friday from 8:00 a.m. to 4:00 p.m., receiving academic support and tutoring for their independent study curricula; along with cognitive and behavioral therapy.  During this time, RESCU Academy acted as a liaison between students and parents, and their schools.  Students were provided with academic support and tutoring, transportation to weekly appointments with their independent study teachers, and treatment and counseling for their substance abuse and/or mental health issues.

In 2003, RESCU Academy received certification as a Non-Public Agency (NPA).  Through the NPA, contracts were developed with several San Diego County school districts including San Diego Unified School District, Poway Unified School District, Grossmont Union High School District, and Sweetwater Union High School District.  RESCU Academy and its students utilized a variety of independent study curricula including those offered by Charter School of San Diego, Home Choice (Grossmont Union High School District), Oracle (San Diego Unified School District), New Directions (Poway Unified High School District), Sunset (San Dieguito School District), and Challenge (Grossmont Union High School District).  As a result of its NPA certification, student enrollment increased. With increased enrollment, the model requiring frequent appointments with home school teachers proved to be unsustainable.  RESCU staff and students traveled so frequently that continuity became difficult.  In order to better serve its students and increase academic hours, the RESCU staff and administrators decided to pursue the development of the school's own individualized curriculum.            

At that point, a certified teacher was employed to assist in the implementation of RESCU Academy's own curriculum, to provide academic support, and to ensure that students were taking appropriate classes to meet their educational goals.  Additionally, the goal for this teacher was to lead the school in the development of individualized curriculum for RESCU Academy. 

In 2004, RESCU Academy worked closely with School Pathways, an educational software developer, to create a state-aligned curriculum for its students. Two certified teachers were employed to implement curriculum through one-on-one instruction, small group work, and peer tutoring.  The school purchased lab supplies and kits to support all high school courses needed for a high school diploma and college prerequisites. RESCU Academy terminated its NPA status and officially became a private comprehensive school through the California Department of Education.

In 2005 and 2006, the teaching staff worked hard to pursue the certifications and accreditations that would ensure the school's population of students was supported by a trustworthy institution.  In 2004, RESCU Academy applied for candidacy for affiliation with the Western Association of Schools and Colleges (WASC).   In 2005, WASC granted RESCU Academy interim accreditation through June 30, 2008.

To meet accreditation expectations that RESCU Academy provide a rigorous and standards-based curriculum, the staff designed courses specifically to meet the course requirements for the University of California a-g course list. This would allow RESCU graduates to qualify academically for admission into the University of California system. In 2006, the school received its initial approved course list. Courses that were not accepted in 2006 were then modified, redeveloped, and resubmitted to the University of California.  Currently, all RESCU Academy courses needed for a high school diploma and to meet the entrance requirements for the University of California and California State University college systems have been approved.

In 2008, RESCU Academy received the maximum accreditation from the Western Association of Schools and Colleges (WASC) until 2014.