This paper explores the association between school-level factors and learning outcomes of children in 361 rural public primary schools of Khyber Pakhtunkhwa (KP) Province, Pakistan. Two datasets have been used for the purpose: Education Management Information System (EMIS) for school-level factors and Annual Status of Education Reports (ASER) for student learning outcomes. The analysis reveals that school size, multigrade schools, teachers' qualification and teachers' attendance are significant predictors of children's numeracy and English reading skills whereas teachers' qualification and teachers' attendance, were found significant across all the three proficiency levels--reading Urdu, reading English and two-digit subtraction.