There has been long discussion in educational psychology about the individual factors that promote pupils' sense of school belonging during secondary education. However, the literature on the school factors associated with these outcomes seems to be less informed. By utilising an ecological-systemic approach, the present study aimed to consider the predictive role of a range of individual and school factors including academic achievement, motivation, gender, class size, extracurricular resources, and type of school attended. To do this, UK data of a large, current and representative sample of 14,157 15-year-old pupils in 550 schools from the Programme for the International Student Assessment (PISA) study were analysed. Using a multi-level structural equation modelling framework, results indicated that the individual-level factors statistically significant associated with pupils' sense of belonging were academic motivation, gender, and socio-economic status, explaining 6% of the student-level variance. School factors that predicted sense of school belonging included availability of extracurricular activities, and class size, explaining 39% of the school-level variance. Our results provide strong evidence concerning the importance of school factors that may be more malleable to change, when compared to individual factors, in determining pupils' sense of belonging. We propose a theoretical framework that integrates the role of individual and school factors to advance knowledge concerning pathways for the development of evidence-based intervention targeting the improvement of school belonging.