Physical exercise is an effective non-pharmaceutical treatment for Parkinson's disease (PD) symptoms, both motor and non-motor. Despite the numerous reports on the neuroplastic role of physical exercise in patients with PD (PwPD), its effects have not been thoroughly explored via brain network science, which can provide a coherent framework for understanding brain functioning. We used resting-state EEG data to investigate the functional connectivity changes of the brain's intrinsic cortical networks due to physical exercise. The brain activity of 14 PwPD before and after a ten-week protocol of computerized physical training was statistically compared to quantify changes in directed functional connectivity in conjunction with psychometric and somatometric assessments. PwPD showed a significant reorganization of the post-training brain network along with increases in their physical capacity. Specifically, our results revealed significant adjustments in clustering, increased characteristic path length, and decreased global efficiency, in correlation to the improved physical capacity. Our results go beyond previous findings by indicating a transition to a reparative network architecture of enhanced connectivity. We present a meaningful relationship between network characteristics and motor execution capacity which support the use of motor treatment in tandem with medication. This trial is registered with ClinicalTrials.gov Identifier NCT04426903.