It was established to provide for more intensive and advanced secondary education program with special reference to science and technology.

The establishment of the Rizal National Science High School was conceived and proposed by then Cong.

On its initial operation (school year 1998−99), 90 scholars (34 boys and 56 girls), six mentors, and two non-teaching personnel from the local government were housed at the Rizal State College Binangonan Campus under the supervision of Remedios C. Gervacio, head teacher III, and Dr. Remedios G. Aquino, science supervisor, as monitoring official.

Science equipment, instructional materials like books, charts, audio-visual resources, tables, chairs etc.

Students joined municipal, provincial, regional and national academic competitions and have brought several major awards.

In December of school year 2001−02 (After the terror attacks on September 11), Genesius Fulgeras took over as the principal.

On April 13, 2024, RNSHS's longest-serving Officer-in-Charge and SHS Registrar (with 23 years of active service), Mrs. Alma Abuacan-Casas, has retired.

RNSHS actively participates annually in contests like Schools Press Conferences, Science Fairs, Essay Writing Contest, Patimpalak ng Sabayang Pagbigkas, Speech Choir Competitions, Oratorical and Extemporaneous Speaking, Water Rocket Events, Tagisang Robotics of the Department of Science and Technology, and other events sponsored by schools, government agencies/units and non-government organizations.

Inspired from the University of the Philippines' Sablay, RNSHS has its version of garb worn during commencement exercises.

Running through the sablay are Baybayin figures of the batch number (in Filipino language) of which a member is a graduate.

Launched by the RNSHS Parents and Teachers' Association (PTA) annually, Mr. and Ms. RiSci is one of the school's most-awaited event.

Its objectives are to showcase the students' beauty, intelligence and talent to the RiSci community and to raise funds for school projects.