The High School Department (LHS & SHS) of the university is part of the College of Education (COED).
The Laboratory High School (LHS) features honors and semi-honors sections. The honor section is section A. The semi-honors classes are sections B, and C, which emphasize Mathematics, Filipino, Science and English. Students who are in those classes will be classmates for the rest of their high school life provided that they do not fail a year. In June 2015, the class sectioning was made heterogeneous where students are not sorted based on their intelligence, but randomly. The ninth graders are to choose one of the major classes; Handicrafts, Automotive, Ceramics, Foods and Garments. They are supposed to stick with their chosen major class until tenth grade.
The LHS also has its governing body, the Student Body Organization (SBO) and its own publication, The Molder.
The Senior High School (SHS) is a new department to cater the Senior High Schools Students under the K-12 Program. Currently there are three tracks/stands offer in the university namely: STEM, ABM, and HUMSS.