This study investigates school discipline practices in senior high schools (SHS) in Misamis Oriental, Philippines, to design a culturally responsive, evidence-based positive behavior management system. Employing a mixed-methods approach with data and methodological triangulation across 42 public and private schools, the research examines leadership influences, program preparation, decision-making sources, and the quality of consequences and motivational strategies. Findings reveal systemic challenges: 60% of schools report inconsistent policies, 70% lack structured planning, 65% rely on non-evidence-based decision-making, and 80% predominantly use punitive consequences. Qualitative data further highlight limited stakeholder involvement and reactive, ad hoc practices. Guided by General Systems Theory, Theory of Action, and Self-Determination Theory, the study proposes a responsive framework integrating four core components—climate and prevention, expectations and consequences, motivation, and equity and continuous improvement—aligned with U.S. Department of Education guidelines and adapted to the Philippine K–12 context. The framework emphasizes stakeholder collaboration, culturally relevant values (e.g., bayanihan, respeto, kapwa), and tiered, motivation-driven interventions. This research fills a critical gap in Philippine education by offering a structured, culturally grounded model to shift from punitive discipline to a proactive, equitable system that supports student well-being, school safety, and DepEd’s child protection agenda.