Motor learning and professional sports training can induce plastic changes in brain structures that are associated with distinct training demands. To testify the hypothesis of that regional gray matter structures in the motor-related cortex and its functional connectivity (FC) are altered in young divers. We undertook T1-voxel-based morphometry (VBM) structural and resting-state functional magnetic resonance imaging in groups of diving athletes (DAs) and demographically-matched healthy controls. Gray matter volume was lower in some regions in Das. By selecting the five most reduced regions, i.e. superior frontal gyrus, orbitofrontal cortex (OFC), insula, hippocampus, and cerebellum posterior lobe, as regions of interest (ROIs) for FC analysis, results showed that DAs had greater FC between the inferior temporal gyrus and superior frontal gyrus, OFC and cerebellum posterior lobe. Conversely, the divers had lesser FC between OFC and putamen, superior frontal gyrus and caudate. VBM differences suggest that diving training entails more effective synaptic and/or neuronal pruning processes in motor structures. Indeed, cortical volumetric decreases in the DAs group are associated with increased FC among certain motor-related regions. We conclude that motor learning in adolescence alters brain structure in association with changes in FC between the relevant cortical and subcortical regions.