Aguinaldo Elementary School is formerly a part of a group of annexes of Murphy Elementary School in 1947. The school site was then occupied by a group of squatters. Since it was a government property, petitions were made by the Teaching Club headed by Mrs. Adoracion Catolico and the officers of the PTA to relocate the squatters and put up a school. With the initiative of the then Quezon City, Mayor Norberto S. Amoranto, the squatters were relocated. The Mayor approved the construction of a six-room building which was finished in 1958. It was in November 1958 when the Grade V and VI classes from the Main Building were transferred to the new school building. Mrs. Wilhelmina P. Abelardo, the Principal, stayed in the old school to attend to the Grades I – IV classes. Miss Deny Gruta, the Assistant Principal stayed with the intermediate classes. Since there were no extra rooms for Home Economics, Industrial Arts, and Canteen, Mrs. Abelardo, Mr. Concepcion Caballero, and Mrs. Rosario Solis made representations with the AFP for the Pre-fab building. The AFP responded and put up a Pre-fab building with three rooms.
It was during the time of the new supervisor assigned in the school in 1955 that the name of the school was officially changed from Murphy Elementary School to Emilio Aguinaldo Elementary School. The Assistant Principal then was Mrs. Ester Fernandez. Through the initiative of Mr. Plan and a group of teachers, actions were made to request for more Pre-fab buildings. These teachers who worked hard were Mesdames Concepcion Caballero, Rosario Solis, Estrella Fernandez, Adoracion Catolico, Cristina Ochosa, Coring Alindogan and Dolores Sedantes. Immediately, the late President Carlos P. Garcia ordered the AFP to put up more Pre-fab buildings. In addition, the First Lady, Leonila Garcia donated some amount for the stage. Later on, these Pre-fab buildings and the stage underwent gradual improvements making them presentable as they are now.
At present, Aguinaldo Elementary School is a complete elementary school catering to Kindergarten and Grades I to VI school goers.