The purpose of this research was to investigate the effect of school facilities on learners’ academic performance in science subjects in secondary schools in Rutsiro district, Rwanda. The following objectives guided the study: The study aimed to investigate the impact of physical facilities and physical instructional materials on students' academic performance in science subjects in Rutsiro district secondary schools. Furthermore, it aimed to investigate the influence of electronic instructional materials on the academic performance of science students in Rutsiro district secondary schools. Environmentalist Bandura's theory of learning, also known as the social cognitive learning theory (SCLT), guided the research. Based on the descriptive research design and mixed-methods approach, the study was conducted in five selected secondary schools in the Rutsiro District. The study's target population consisted of 460 respondents: five head teachers, five directors of studies, 150 teachers, and 300 students. The study involved 214 participants, including 2 head teachers, 2 directors of studies, 70 teachers, and 140 students. Systematic sampling was used to select the five schools, purposive sampling to select the student sample size, and the census sampling technique to select the head teachers and directors of studies. Data was collected using structured questionnaires, interview guides, and documentary reviews. The data was analyzed using descriptive statistics (frequencies, percentages, mean, and standard deviation) and inferential statistics. The study found a significant correlation between the availability of school facilities and academic performance. There were positive and significant correlations between academic performance and school facilities in Rutsiro District, Rwanda, and measures of the availability of school facilities were as follows: physical facilities (r = 0.814, p<0.01), electronic and technology facilities (r = 0.826, p<0.1), and physical instructional materials (r = 0.949, p<0.01). The findings from regression analysis revealed that physical facilities have a positive and significant effect on learners’s academic performance in science subjects in Rutsiro district secondary schools (β = 0.814, P value <0.05), The findings from regression analysis revealed that physical instructional materials have a negative and significant effect on learners’s academic performance in science subjects in Rutsiro district secondary schools (β = -0.417, P value <0.05), The findings from regression analysis revealed that electronic instructional materials have a positive and significant effect on learners’s academic performance in science subjects in Rutsiro district secondary schools (β = 0.308, P value <0.05). Teachers, district education officials, and head teachers all agree that school facilities influence academic performance in science subjects positively. Specifically, physical facilities motivate learners and enhance their performance. It was observed that students taught in classrooms equipped with school facilities outperformed those without access. Consequently, the study recommends that science teachers utilize available school facilities for instruction and adapt when materials are unavailable.