In 1947 Mr.Pablo Reyes, principal of Torres High School pushed through with his plan of separating Ismar Annex from Torres High School because of its increasing population. On June 16, 1958 the annex became Ismar High School. This was in accordance with Division Memorandum No.60 s.1958. The new school was supervised by Mr. Fabian Bugayong as second principal, Leonor Zapanta as head teacher and Mr. Aurelio Libao as guidance counselor. There were 66 teachers and a population of 1,425 students.
On September 25, 1958 then mayor Arsenio H.Lacson approved Resolution No. 529 changing Ismar High School to Gregorio Perfecto High School in honor of the late Supreme Court Associate Justice Gregorio Perfecto, one of the signatories of the 1935 Constitution who used to represent Tondo in Congress.
Unfortunately, the building was damaged by an earthquake in 1969, then another one in 1990 that led to the total reconstruction of the school building. The reconstruction lasted for three years. But during the reconstruction period classes went on. The first and second levels were housed at the Tondo Sports Complex, the third year in a vacant lot located at Ricafort St. where makeshift rooms were put up, and the fourth year at the Manuel L. Quezon Elementary School.
The school building was finally restored in 1993. A fire destroyed the third floor on December 6, 1996. The third floor of the school building was restored and was inaugurated on September 17, 1997.