Mindfulness-based programs have become popular, empirically supported treatment modalities for increasing positive psychological outcomes for children and adolescents, with an overall effect size of 0.4. We argue for implementing community-based participatory research (CBPR) methodology to investigate the specific effects of mindfulness-based intervention (MBI) programs within schools. While interest in MBIs in schools has resulted in their increased application, research based on CBPR methodology can fill several gaps in the existing literature by collaborating with school personnel and viewing teachers, students, and staff members as equal research partners. A CBPR approach could help recognize individual differences and contextual factors that often inhibit MBI success, as well as address implementation issues, interventionist factors, and fill the science-to-practice gap. We end by providing practical information to help translate CBPR approaches into the school setting.