Objective: Recent studies have shown promising effects of physical activity on cognitive function, but there is a need to investigate this link in real-life settings such as schools. Hence, the objective of the present pilot study was to investigate whether the school-based physical activity programme “FIFA 11 for Health” for Europe could improve cognitive performance in preadolescent Danish children. Methods: The pilot study used an 11-week cluster-randomised intervention study design. School classes were randomly assigned to either a control group (CG) (n = 93 children, age = 11.8, s = 0.2 years), which performed the obligatory daily school-based physical activity (5 × 45 minutes per week); or an intervention group (IG) (n = 838 children, age = 11.9, s = 0.4 years), which substituted 2 × 45 minutes per week of the daily school physical activity with the “FIFA 11 for Health” for Europe programme. The programme combines small-sided football games, drills and health education. Cognitive performance was evaluated at baseline and follow-up. Results: The IG improved their cognitive performance compared to the CG for psychomotor function (56, sx– = 22 ms, p < .001), attention (39, sx– = 17 ms, p = .012) and working memory (79, sx– = 35 ms, p = .020). Conclusion: This pilot study provides evidence that the school-based physical activity programme “FIFA 11 for Health” for Europe can improve cognitive performance in preadolescent Danish schoolchildren. Future studies should attempt to disentangle the effects of “FIFA 11 for Health” for Europe on cognitive performance by investigating the characteristics of the programme’s physical activity.