Physical exercise can evoke changes in the brain structure. Consequently, these can lead to positive impacts on brain health. However, physical exercise studies including coordinative exercises are rare. Therefore, in this study, we investigated how 12 weeks of physical exercise breaks (PEBs) with coordinative exercises, focusing mainly on juggling tasks, affected the brain structure. The participants were randomly allocated to an intervention group (IG, n = 16; 42.8 ± 10.2 years) and a control group (CG, n = 9; 44.2 ± 12.3 years). The IG performed the PEBs with coordinative exercises twice per week for 15-20 min per session. Before the intervention, after 6 weeks of the intervention, and after 12 weeks of the intervention, participants underwent a high-resolution 3T T1-weighted magnetic resonance imagining scan. Juggling performance was assessed by measuring the time taken to perform a three-ball cascade. A surface-based analysis revealed an increase in vertex-wise cortical depth in a cluster including the inferior parietal lobe after 6 and 12 weeks of training in the IG. After 12 weeks, the IG showed a decrease in gray matter (GM) volume in a cluster primarily involving the right insula and the right operculum. The changes in the GM volume were related to improvements in juggling performance. No significant changes were found for the CG. To conclude, the present study showed that regular engagement in PEBs with coordinative exercises led to changes in brain structures strongly implicated in visuomotor processes involving hand and arm movements.