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Introduction Persistent underperformance in mathematics remains a critical challenge in South African secondary schooling, as consistently evidenced by successive cycles of the Trends in International Mathematics and Science Study (TIMSS). While socioeconomic inequality and resource disparities are well-established explanations, less empirical attention has been given to how school safety conditions, as perceived by students, shape mathematics learning environments. Methods This study examined the association between school safety factors and Grade 9 mathematics achievement in South Africa using nationally representative TIMSS 2023 student self-report data. The study was guided by an integrated conceptual framework that combines Scheerens' input-process-output model with Bronfenbrenner's Ecological Systems Theory, positioning school safety as a key contextual input that is associated with achievement through teaching and learning processes. A quantitative secondary data analysis was conducted using multilevel modeling to account for students nested within schools. The sample comprised Grade 9 students from South African schools participating in TIMSS 2023. Data were drawn from mathematics achievement scores and student questionnaire items capturing experiences of intimidation, social exclusion, coercion, physical violence, and cyber victimization. Results The results indicate that several safety-related experiences, particularly social exclusion, coercion, cyber victimization, and physical harm, were significantly and negatively associated with mathematics achievement, with cyber victimization showing particularly strong associations. An unexpected positive association was observed between reported theft and mathematics achievement, and some suggestions are provided as to why this may be the case. Discussion The study provides large-scale empirical evidence that school safety is a significant contextual factor associated with mathematics achievement, highlighting the importance of integrating safety considerations into educational improvement strategies.