This study assessed the performance of substitute teachers as perceived by school heads, identified the challenges they encountered, and developed a school-based intervention program to enhance their teaching performance. The study was conducted in selected public secondary schools in Zone 3, Division of Zambales during the School Year 2025–2026. A descriptive research design utilizing a quantitative approach was employed in the study. Data were gathered through a structured questionnaire administered to 24 school heads and 135 teacher-respondents who had experience serving as substitute teachers. The instrument measured substitute teacher performance across seven domains: Content Knowledge and Pedagogy, Learning Environment, Diversity of Learners, Curriculum and Planning, Assessment and Reporting, Community Linkages and Professional Engagement, and Personal Growth and Professional Development. It also determined the challenges encountered in terms of Preparation and Lesson Delivery, Classroom Management, Student Engagement and Motivation, Support and Resources, and Professional and Personal Concerns. Statistical tools such as frequency, percentage, weighted mean, and Analysis of Variance (ANOVA) were used to analyze the data. Findings revealed that the majority of the school head-respondents are female, belong to the middle-aged group, hold positions such as Principal I and Principal III, and have 7–15 years of teaching experience. Most of the teacher-respondents are female, early to middle adulthood stage, and have educational backgrounds primarily in secondary education majors. The majority have 7–15 years of teaching experience, have served as substitute teachers 2–5 times, and have experienced substitution for more than one month. Substitute teachers were generally competent across all performance domains, as perceived by school heads. However, they sometimes encountered challenges, particularly in preparation and lesson delivery, classroom management, and student engagement. The results of the ANOVA showed that most demographic variables did not significantly affect substitute teacher performance and challenges, except for a few cases such as position in curriculum and planning, years of teaching in classroom management and student engagement, and sex and years of teaching in support and resources.