The retinal microcirculation serves a proxy of cerebrovascular function and has been linked with both physical fitness and cognitive function. We investigated the role of physical fitness for the development of executive function in children as well as its mediation by microvascular health. Using a cross-lagged panel design, 365 children aged six to eight years completed a baseline assessment, which was followed up after four years. Retinal vessel analysis was performed on digital retinal images obtained with a fundus camera. Additionally, a computerized Flanker task was administered to assess the inhibitory aspect of executive function. With regard to physical fitness tests, participants completed a shuttle run and 20-m sprints. Path-analyses showed that higher performance on the shuttle run and 20-m sprint at baseline were both associated with lower reaction times on the Flanker task at follow-up, when autoregressive effects were accounted for. Stages achieved on the shuttle run at baseline were further related to narrowing of retinal venular diameters, which in turn predicted performance on the Flanker task. However, the direct relation of physical fitness components to reaction time was higher compared to the indirect relation via retinal venular diameters. High physical fitness contributes to the development of cognitive abilities from childhood to preadolescence. This association is not mediated by retinal vessel diameters, while the microvascular phenotype of narrower retinal venules is independently related to a better development of information processing and inhibitory control.