The school was founded and established in 1988 per Ordinance No. 81, Resolution No. 6 dated August 10, 1988, upon the recommendation of the Board of Directors of the Dumaguete Science Foundation, Inc. which is the resourcing arm of the school to maintain and sustain its operation. RTPM - Dumaguete Science High School, started as a single-level and single-class high school temporarily occupying an area within the campus of the
Dumaguete City National High School in Calindagan. It moved to its permanent school site in Villa Amada Subdivision of Barangay Daro on land donated by Ramon Teves-Pastor, in 1991 and has since grown from a single classroom within other city schools to a complete high school of more than 40 students. On July 21, 1993, the RTPM – Dumaguete Science High School was integrated into the national roll by virtue of DECS Order No. 69, s. 1993 as among the thirteen
Regional Science High Schools throughout the country (now composed of sixteen regions). It is one of the top high schools in the region. The school also served as Regional Science High School for the short-lived Negros Island Region (Region XVIII) under the new setup of the national government to establish DepEd Regional Office in Dumaguete. However, the region only existed from May 29, 2015, through Executive Order No. 183 signed by President
Benigno Aquino III and later abolished by President
Rodrigo Duterte on August 9, 2017, through signed Executive Order No. 38 to revoke EO No. 183. DepEd Regional Office for Negros Island Region in Dumaguete became what is now the DepEd Sub-Regional Office of Region VII when the province of Negros Oriental returned to Central Visayas and the school once again served as RSHS for its original region. In 2016, the school was extended to include a senior high school teaching up to grade 12. ==Facilities==