The aim of the present study was to determine the effect of 5-weeks participation in The Daily Mile on cognitive function, physical fitness, and adiposity in primary school children. In a quasi-experimental study, one class from each school completed The Daily Mile (n = 44) or acted as a control group (n = 35). Baseline measures included cognitive function tests (Stroop test, Sternberg paradigm, Flanker task), physical fitness (multi-stage fitness test) and body composition (BMI percentile, waist:hip circumference, sum of skinfolds). The intervention group completed 5-weeks of The Daily Mile. Follow-up measurements were completed within 48-h of the last training session. Data were analysed via ANCOVA, examining between group differences at follow-up, controlling for baseline values. Response times on the complex Stroop test were faster at follow-up in the intervention group (Intervention: 1357 ms [1280–1400 ms]; Control: 1463 ms, [1410–1523 ms], d = 0.31, p = 0.048). There was no effect of The Daily Mile on the Sternberg paradigm or Flanker test. Physical fitness was greater at follow-up in the intervention group (Intervention: 880 m, [820–940 m]; Control: 740 m, [680–800 m], d = 0.39, p = 0.002). There was no effect of the intervention on adiposity. In conclusion, five-weeks of The Daily Mile enhanced inhibitory control and physical fitness in children, but did not affect working memory, attention, or adiposity.