The beneficial effects of physical activity on neurocognitive functioning in children are considered to be facilitated by physical activity-induced changes in brain structure and functioning. In this study, we examined the effects of two 14-week school-based exercise interventions in healthy children on white matter microstructure and brain activity in resting-state networks (RSNs) and whether changes in white matter microstructure and RSN activity mediate the effects of the exercise interventions on neurocognitive functioning. A total of 93 children were included in this study (51% girls, mean age 9.13 years). The exercise interventions consisted of four physical education lessons per week, focusing on either aerobic or cognitively demanding exercise and were compared with a control group that followed their regular physical education program of two lessons per week. White matter microstructure was assessed using diffusion tensor imaging in combination with tract-based spatial statistics. Independent component analysis was performed on resting-state data to identify RSNs. Furthermore, neurocognitive functioning (information processing and attention, working memory, motor response inhibition, interference control) was assessed by a set of computerized tasks. Results indicated no Group × Time effects on white matter microstructure or RSN activity, indicating no effects of the exercise interventions on these aspects of brain structure and function. Likewise, no Group × Time effects were found for neurocognitive performance. This study indicated that 14-week school-based interventions regarding neither aerobic exercise nor cognitive-demanding exercise interventions influence brain structure and brain function in healthy children. This study was registered in the Netherlands Trial Register (NTR5341).