As an annex of FABC High School Department, it started with four (4) teachers teaching four (4) First Year classes at old Mater Dolorosa (now Mirror of Justice) Church along Aguho St. Comembo. The head teacher then was Miss Tomasa Sinad, a former nun.
Miss Sinad did not stay for long as she migrated to the United States. She was succeeded by Mrs. Percida Dela Cruz as Officer-in-Charge and as Department Head of Filipino Department in concurrent capacity. Not for long, Mrs. Dela Cruz was recalled to her mother school to concentrate as fulltime Department Head and was succeeded by Mrs. Remedios C. Pajo.
Successively, BNAHS has been under the helm of other educators that followed namely: Dr. Nora H. Serdena, Mr. Wilmore C. Moredo, and Dr. Reynaldo S. Estacio.
The following year, it offered, a second year class , then it added one third year class the following year until finally in 1979, FABC High School Department - Comembo Annex held its first graduation ceremony in the plaza of the Comembo Elementary School.
After a year, the school transferred to the prefabricated building constructed by soldiers in Lanzones St. in Comembo. Classes continued there on until a new four-storey building was constructed under the administration of Mayor Jejomar C. Binay with Dr. Nora Serdeña as Officer in-Charge.
On January 25, 1993 at a consultative meeting of the Sangguniang Barangay ng Comembo headed by Barangay Captain Pedro Daza and the General P.T.A. President of the school, Mr. Felix Garcia, a joint resolution was passed requesting the Municipal Council, thru Mayor Jejomar C. Binay that FABC High School Department – Comembo Annex be Converted to an independent community or barangay high school. The motion was filed by Mr. Garcia and duly seconded by Kagawad Ernesto Aguilar.
The Makati City Council approved the City Ordinance 74-278 series of January 13, 1995 creating an independent municipal high school and renaming FABC High School Department - Comembo Annex as BENIGNO “Ninoy” S. AQUINO HIGH SCHOOL.
The name was carefully chosen because the city council felt that “nothing is more fitting than to name the school after “Ninoy”, the man, imbued with courage, gallantry, patriotism and devotion to country, made the greatest sacrifice a person could ever make, that of offering his life so others would be free.
He was the only man who broke the conjugal dictatorship, united his fellowmen with his death to stand up against martial rule. Without him, freedom for the Filipino people would have remained an elusive dream. His life has become an inspiration to all, especially to our students who know all his struggles and ambition.”
Initially, BNAHS used to be a non-subsidiary of the national government. Its teachers, however, were classified in the same salary grades just like the other teachers paid by the national government.
On May 06, 1998, the Plantilla of personnel of BNAHS was then approved by DECS. Likewise, it was nationalized and the existing positions were found to be in accordance with National Budget Circular No. 458, series of 1997.
In June 1994, Dr. Nora H. Serdena became the Principal of Benigno “NinoY” S. Aquino High School. There were only 15 classes organized as there was only a four-storey building. Moreover, there were just 26 teachers handling the classes. Since the school at that time could not absorb all the elementary school graduates in its catchment areas – namely: Pembo Elem. School, Comembo Elem. School, Tibagan Elem. School, East Rembo Elem. School and Rizal Elem. School, Mayor Jejomar C. Binay decided to switch the locations of Comembo Elementary School and Benigno Aquino High School.
At present,Comembo Elementary School is situated at Lanzones St.,Barangay Comembo. On the other hand, BNAHS has expanded its site in the old Comembo Elementary School having 6 school buildings to accommodate the growing number of students within the area. The school site was much wider with an area of 13,060 square meters. The quadrangle was indeed suitable for holding CAT drills, PEHM classes and other school related activities.
The completion of the new school building saw the coming of the new Principal in the person of Dr. Reynaldo S. Estacio. With the completion of Bldg VI, the school now has additional classrooms that were used starting SY 2006-2007. Some of the new facilities include laboratory rooms, computer laboratories for the three core subjects (English, Math and Science), TLE rooms/shops and several other function rooms.
With these facilities that complement the academic formation of the students, the effective leadership of its Principal, Dr. Reynaldo S. Estacio, together with the competent and committed Department Heads and teachers has excellently carried out the School Improvement Plan to fulfill its mission and vision. This is precisely the reason for considering BNHS as a high performing school in Makati.