Marikina Science High School was founded on 18 July 1947 as Marikina Junior High School through Municipal Council Resolution No. 59 s. 1947. This is done to jump start higher education in the town of Marikina, which was then under the administration of Gil Fernando. Fernando then became regarded as the “Father of secondary education” in Marikina, who worked together with Tomas L. Santos after World War II to recognize his integrity, eloquence and learning for the rehabilitation of schools.
In 1952, it changed its name to the Leodegario Victorino Memorial High School (LVMHS) in honor of Leodegario Victorino, former councilor of Marikina, Marikina School of Arts and Trades (MSAT) in 1957, and Marikina Institute of Science and Technology (MIST) in 1978. This is where Marikina Science High School traces its origin. On November 8, 2001, the secondary level was separated from Marikina Institute of Science and Technology, giving way to the establishment of what is now Marikina Science High School. Meanwhile, through Republic Act 9289, the college sector of MIST was renamed as Marikina Polytechnic College (MPC) in 2004.