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, at the request of members of the treatment program, RESCU Academy became a full-time school support program in which students attended the program every day from 8:00 a.m. to 4:00 p.m. and received academic support and tutoring for their respective independent study curriculum; along with cognitive and behavioral therapy.  During this time, RESCU Academy acted as a liaison between students, 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, 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 the students of RESCU Academy, and to increase academic hours, the staff and administrators decided to pursue the development of their 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 creator, 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 thereby 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 as many certifications and accreditations as they could to ensure their 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.

In an effort to meet the accreditation expectations to have a rigorous and standards-based curriculum, RESCU Academy 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 originally 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 on the UC a-g course list for the 2007-2008 school year.