Aupagan Elementary School is located 8.8849⁰ N , 125.5649⁰ E, Barangay Aupagan, Butuan City, Agusan del Norte. And it is approximately 11 kilometers from the city proper. It has a total land area of 1 hectare and besides Aupagan National High School.

Aupagan Elementary School first opened in 1950.It was in 1954 when the first school site Agusan River was formally donated by Honorato Cawilan to the City of Butuan. The school was a complete elementary then because the barangay was log pond of logging company which was operating nearby forest, when logging company stopped its operation in 1960, the enrolment was affected and so school became a primary school with only two (2) teachers.

The late Punong Barangay Hon. Efren A. Martinez, Sr., realized the hazards of a school at the bank of Agusan River and so the family donated a one (1) hectare lot located in Purok 5 Upper Aupagan, Butuan City for a new school site. The new site is one (1) kilometer away from the river bank and from the old school site the year 1988. In that same year Grade –V was reopened occupying a makeshift room in the site. In the following year, two building was constructed. After 3 years, all grades moved to the new school site. In March 1994 the school had first graduation exercises after reopening.

In the year 2009, as initiated by the Principal, Mrs. Rosemarie B. Bahan, opened the Preschool with 50 pupils under the advisory of a PTA funded teacher. In June, 2009 in same year opened a First Year High School with 41 students under a volunteer teacher Mr. Pergentino B. Cabahug, III, who is funded by the Barangay Council of Aupagan. The succeeding year, Second Year was opened then Third Year until such it completed until Fourth Year High School. The school that time was named Aupagan Integrated School.

The Principal after Mrs. Bahan was Mr. Angel A. Pitogo, Sr. who led the processing of needed

documents until such the high school was granted to be a nationalized high school.

This time, the school was name back to Aupagan Elementary School in 2015.