Berries contain bioactive compounds that may affect children’s cognitive function positively, while hunger and thirst during lessons before lunch affect academic performance negatively. This pilot study addresses methodological challenges in studying if a berry smoothie, offered to schoolchildren as a mid-morning beverage, affects academic performance.The objective was to investigate if a cross-over design can be used to study these effects in a school setting.Therefore, in order to investigate assay sensitivity, 236 Swedish children aged 10–12 years were administered either a berry smoothie (active) or a fruit-based control beverage after their mid-morning break. Both beverages provided 5% of child daily energy intake. In total, 91% of participants completed the study. Academic performance was assessed using the d2 test of attention. Statistical analyses were performed using the Wilcoxon signed rank test in StatXact v 10.3.The results showed that the children consumed less of the active berry smoothie than the control (154 g vs. 246 g). Both beverages increased attention span and concentration significantly (p = 0.000). However, as there was no significant difference (p = 0.938) in the magnitude of this effect between the active and control beverages, the assay sensitivity of the study design was not proven. The effect of the beverages on academic performance was attributed the supplementation of water and energy.Despite careful design, the active smoothie was less accepted than the control. This could be explained by un-familiar sensory characteristics and peer influence, stressing the importance of sensory similarity and challenges to perform a study in school settings. The employed cross-over design did not reveal any effects of bioactive compound consumption on academic performance. In future studies, the experimental set up should be modified or replaced by e.g. the parallel study design, in order to provide conclusive results.