The original academic program of the university, the Integrated School's elementary and high school programs opened in 1907. The programs were closed in its Mendiola Campus in the mid-1990s and formally phased out in 2004 in its Malolos campus. The last batch of its elementary and high school students were from its Malolos Campus in 2004 and 2001, respectively. The university will once again offer the Integrated School in its Malolos Campus starting the school year 2014-2015.
On its first year of re-operation the University Integrated School will offer Nursery, Pre-Kindergarten, Kindergarten, Grade 1 and 7. While on the following year, the school opened its Grade 11 and 12 in compliance of the k-12 system.