| Scholarship | Qualifications | Benefits |
| College | ||
| Presidential Scholarship | Awarded to select high school valedictorians | 100% free tuition and fees for 4 or 5 years, depending on course. P1,000 monthly allowance for student. P1,000 monthly educational support for student's family. |
| In-residence Academic Scholarship | Top 25 in Dean's List. Must not have been suspended during the previous term for disciplinary reasons | Full tuition scholarship for succeeding term for Top 10 on Dean's List (not including Presidential, Academic, OJH, and other academic scholarships) Half tuition scholarship for succeeding term for Top 11 to 25 on Dean's List (not including Presidential, Academic, OJH, and other academic scholarships) |
| Entrance Scholarship - HS Valedictorian | High school class valedictorian | Full tuition scholarship |
| Entrance Scholarship - HS Salutatorian | High school class salutatorian | Half tuition scholarship |
| Student Assistantship (includes Student Marshals) | Student must be a member of a family whose annual gross income ≤ P200,000. Must have no failing grade. Good moral conduct. Must not have been suspended the term and year before for disciplinary reasons. Fit to work. Must pass screening and interview. | Full tuition scholarship for a maximum of 21 units per term. This is renewable depending on performance. |
| Alumni Scholarship | Student must be a child of a PEN School graduate. | 10% tuition fee scholarship every term except summer |
| PD 577 | See PD 577 | Full tuition scholarship |
| Basic Education | ||
| Presidential Scholarship | Awarded to select grade school valedictorians | 100% free tuition and fees for 4 years. P500 monthly allowance for student. P500 monthly educational support for student's family. |
| In-residence Academic Scholarship | Must have the highest GPA in his class (batch). Must not have been suspended in the previous year for disciplinary reasons. Elementary: Must have a grade of at least ¶¶ in all Traits. Secondary: Must have a grade of at least C in all Traits. Good moral | Full tuition scholarship for 1 year |
| Entrance Scholarship - GS Valedictorian | Grade school class valedictorian | Full tuition scholarship for 1 year |
| Entrance Scholarship - GS Salutatorian | Grade school class salutatorian | Half tuition scholarship for 1 year |