Background: Although active workstations, such as desk bikes, have proven to be beneficial for health, there is limited information regarding their effects on children’s acute cognitive performance during self-paced exercise. Methods: This study used a within-subjects, fully counterbalanced design with a sample of 38 preadolescent children (mean age = 12.50 y, SD = 0.62; 43% male), who performed cognitive tests while being seated or while cycling for 45 minutes with a 7-day interval. Effects of using a desk bike were evaluated on cognitive control: verbal and visuospatial working memory capacities were tested, and inhibition was assessed using a modified flanker task. In addition, subjective task experience was explored using self-report measures. Results: Cognitive control performance was not degraded but also not improved with the short-term use of desk bikes. Because of the null effects, there is no direction and magnitude of the outcomes to discuss. Conclusions: These findings suggest that schools can successfully implement desk bikes to increase physical activity and reduce sedentary time among children without compromising cognitive control processes necessary for academic achievement.