Combining physical fitness (PF) and academic content can be a beneficial way to improve PF and mathematics performance of learners. The purpose of the current study was to establish whether a physically active academic intervention had an effect on the PF and mathematics performance of Grade 1 learners over 16 weeks. This intervention is based on an educational approach that combines physical activity into the academic environment. The goal is to enhance learning by learning through movement. Grade 1 learners [N = 119] from two schools in the southern suburbs of Cape Town, South Africa, volunteered to participate in this study. They were assigned randomly to an attentional control [n = 51] and an experimental group [n = 68]. Pre- and post-test data were collected with the Fitnessgram which measured their PF and the VASSI Mathematics Proficiency Test which measured their mathematical performance. The intervention included age-appropriate PF components that were incorporated into learners' academic lessons. The results indicated that the experimental group performed significantly better (p < 0.01) in mathematics and upper body strength after the intervention. It could be assumed that these improvements can be attributed to the physically active academic intervention programme. These findings suggest that these types of interventions could encourage physical activity (PA) and enhance the PF and mathematical performance of young learners. The current study adds to South African Sport Science literature because it is one of few studies performed in this field that have produced significant results.