A considerable proportion of mental health problems surface in early childhood and adolescent years, with early onset mental health problems having the potential to affect the long-term development of young people. Research shows that positive teaching and learning school climates are associated with positive socio-emotional, behavioural, and academic student outcomes. The pedagogical intervention Teaching at the Right Level (TaRL) creates an enabling learning environments through fun and engaging, targeted instruction—proven to improve foundational numeracy and literacy outcomes of young people. With the current gap in policy relevant mental health and education data in low resource settings, this paper studies the effect of targeted instruction interventions such as TaRL on the mental health and educational outcomes of primary school learners in Botswana. Using a difference in difference design, the study finds that exposure to the learning pedagogy reduces the behavioural and emotional difficulties of children by .15SD when compared to children not yet exposed to the programme. This paper is able to connect the mental health and education literatures, contributing to the evidence base on improving student outcomes.