The offering of Secondary Education was initiated by the Provincial Board of Batanes during the term of Governor Vicente Barsana.

However, in June 1917, with Lucas Gonzalo as Governor, the Batanes High School was formally opened, having the following teacher Mr. Eligio Llanes, Mr. Elpidio Fadri, and Mr. Francisco Asidao.

These were Felix Agusto, Antonio Alcantara, Fernando Baroña, and Jose Baroña, all four from Ivana; and Francsisco Elep, Custodio Villalva, Pedro Hontomin, and Cirilo Faberes who were from Sabtang and a lone female student from San Fabian Pangasinan, Concordia Erefe.

All of these schools offered the Revised Secondary Education Curriculum graduating its students and managing their finances.

On August 22, 2000, the bill sponsored by Congressman Florencio B. Abad – R.A. 8855 was finally passed by Congress and Approved by President Joseph Ejercito Estrada, formally converting the Batanes National High School into the Batanes National Science High School.