The global pandemic of childhood physical inactivity and the associated reduction in physical fitness have become the major health problem. Based on such background, there is growing interest in child development research to investigate the associations among physical fitness, cognitive function, and the underlying neurobiological mechanisms. In the present narrative review, we first summarize the findings from behavioral studies that examined the relations of childhood fitness to academic performance and executive function. Because these behavioral findings remain controversial due to methodological inconsistencies, we further discuss differences in independent variables (e.g., physical activity vs. fitness), confounders (e.g., socioeconomic status), study designs (e.g., cross-sectional vs. randomized controlled trial), and assessments used to measure academic performance and executive function (e.g., task difficulty). Subsequently, we introduce neuroimaging studies on brain volume, task-evoked brain activation, and white matter fiber integrity which may provide mechanistic insights into the behavioral observations. To date, several randomized controlled trials using advanced imaging techniques showed that regular physical activity may change brain activations during executive function tasks and improve white matter fiber integrity in children. Collectively, our literature review suggests that regular physical activity leading to increase in physical fitness is likely to contribute to healthy brain development. Nevertheless, the current evidence is still limited and inconclusive, thus further rigorously designed randomized controlled trails are needed to clarify the association between childhood fitness and brain development.