Japan and Denmark represent two different educational cultures. Where Danish students in general report high scores on self-esteem, Japanese children report low. A student-centered and interaction-based prosocial intervention program that was designed according to Danish educational culture was administered to children aged 11–12 years in Japan. Questionnaires measuring the children’s quality of life (QoL) and metacognitive awareness were applied. Overall, the results showed that the student-centered intervention improved the emotional well-being aspect of QoL among Japanese boys. In contrast, Japanese boys’ scores on the declarative knowledge of metacognitive regulation declined. The teachers’ attitudes towards the intervention program were analyzed by use of interviews. The effect of the student-centered intervention program is discussed with respect to the educational cultures in Japan.