This research investigates the variation and causes of low student performance and weak pedagogical practices, focusing on teaching effectiveness of science and mathematics in Pakistan. Using a mixed methods approach, the study examines how pedagogical practices mediate relationships between relevant factors and student learning outcomes. The findings can inform teacher capacity development policies and guide federal (NACTE) and provincial teacher training institutions in revising teacher education curricula, supporting evidence-based strategies to improve learning outcomes and advance progress towards SDG-4.