The main goal of the current paper was to determine the effects of perceived school climate dimensions (leadership, relationships, professional learning-teaching climate, safety, and physical environment) on students' learning performance in upper primary schools. Correlational design consisted of structural equation modeling with mediation analysis was applied. Three hundred twenty-eight randomly chosen teachers and pupils from upper primary schools of Injibara and Chagni, Awi zone of Ethiopia participated. The 16-item school climate scale that was employed had an internal consistency score of 0.91 according to Cronbach's alpha. To create a well-fitting measurement model, as well as to ascertain the convergent and discriminant validities and the composite reliability of school climate domains, confirmatory factor analysis was carried out. Together, the five school climate factors explained 19% variation on student academic performance. Academic achievement of students was directly and significantly influenced by school leadership and the professional learning-teaching environment. Pupils' academic success was significantly and favorably directly impacted by the overall perceived favorable school climate. Positive professional learning-teaching environment fully mediated effect of physical setting and safety on learning achievement, even though it partially mediated the effect of leadership practice of school. Contribution of positive school climate elements to student's learning achievement should also be further investigated using longitudinal multilevel structural equation models.