Schools devote considerable attention in identifying and implementing evidence-based prevention programmes to enhance student development and functioning. A major challenge faced is with organising the theory, research and practice of the implementation and dissemination process. This poses even greater challenges to schools because these are complex systems and rarely implement programmes singly to meet the varied needs of their students. Beyond establishing efficacy, there is little documentation about how these programmes have been adapted for diverse student populations. We utilised the Prevention System Support component of Wandersman et al.'s (Am J Community Psychol 41:171-181, 2008) Interactive Systems Framework for Dissemination and Implementation to systematically elicit key general and programme-specific capacity builders that promote the implementation of school prevention programmes in Singapore schools. SWOT analysis completed by 308 school programme leaders yielded five organisational-level general capacity builders and two programme-specific factors related to teacher training and technical support. Fewer opportunities and threats present as challenges to strengthening school capacity to deliver programmes effectively. Implications arising from the analysis were discussed.