This study aimed to identify what impact a novel approach to teaching physical education (PE) had on children's physical activity (PA), coordination and cognition compared to current provision. One hundred and fifty children were recruited from six primary schools in Scotland. Outcome measures were the Cognitive Assessment System, the Physical Activity Habits Questionnaire for Children and fundamental locomotor skills (crawling, creeping, marching and skipping). Pre-, post- and 6-month follow-up testing was conducted and data analysed comparing a control and an intervention group. Each group received 2 hours of PE each week during the 16-week intervention. Current provision in PE was delivered in the control group and a Better Movers and Thinkers approach to PE delivered in the intervention group. Significant effects of intervention relative to the control group were identified in cognition (p = 0.001, d = 0.76) and coordination (p = 0.001, d = 0.97). No significant effects of intervention were identified for PA (p = 0.200, d = 0.24). The improvement in the outcome measures remained at the 6-month follow-up testing. The present study has identified cognitive and coordination improvements as a result of a novel PE intervention with benefits maintained 6 months later. This supports the need for modification in current PE provision to optimise the potential for learning across the curriculum.