Various investigations have applied meditation protocols in the school context, with beneficial effects. Transcendental meditation, however, received little attention in primary school settings and few controlled studies are available. The present study is aimed: 1) to investigate the implementation of a school protocol (Quiet Time-QT) based on Transcendental Meditation ™ in a primary school setting 2) to test its efficacy in promoting strengths and resilience in children, using a controlled research, with a cross over design. 92 students attending fourth and fifth class of a primary school were assigned to either the QT intervention, or to a waiting list condition. Children assigned to the waiting list received the QT protocol after few months. Before and after the intervention children were evaluated by their teachers using the Strengths and Difficulties Questionnaire (SDQ) and the Devereux Student Strengths Assessment (DESSA). A Repeated Measures MANOVA was applied to compare the two groups. After the QT intervention children in the experimental condition showed fewer emotional and behavioral difficulties (SDQ) compared to children in the waiting list. An overall positive effect of QT was observed in the total sample in improving children’s strengths and emotional well-being. Participants enjoyed the practice of meditation in the school setting. Conclusions: the results of this controlled investigation showed that the QT school protocol is feasible in the school setting, and it yielded improvements in children’s strengths and well-being. Meditation programs could be easily included in the educational system to sustain children positive development.