This study explored age and gender as moderators of the effects of a school-based mindfulness program on Filipino youth’s depressive and anxiety symptoms; and emotion regulation capacities. Using a randomized controlled trial design; 186 public school children in the Philippines aged 9–16 were randomly assigned to either 8 weekly sessions of a mindfulness program or 8 weekly sessions of a handicrafts program as an active control condition. Simple moderation analyses using PROCESS macro indicated that age and gender were significant moderators. Specifically; the mindfulness intervention was more effective for older children than younger children in alleviating difficulties in impulse control; emotional acceptance; and use of emotion regulation strategies. In addition; the mindfulness intervention was more effective for girls than boys in improving anxiety symptoms and emotional acceptance. These findings highlighted the need to consider participant characteristics such as age and gender in designing and implementing mindfulness-based intervention programs in the school context.