We sought to investigate whether regular balance training of moderate intensity (BT) has an effect on changes in selected cytokines, neurotrophic factors, CD200 and fractalkine in healthy older adults and participants with Parkinson’s disease (PD). Sixty-two subjects were divided into groups depending on experimental intervention: (1) group of people with PD participating in BT (PDBT), (2) group of healthy older people participating in BT (HBT), (3,4) control groups including healthy individuals (HNT) and people with PD (PDNT). Blood samples were collected twice: before and after 12 weeks of balance exercise (PDBT, HBT), or 12 weeks apart (PDNT, HNT). The study revealed significant increase of interleukin10 (PDBT, p = 0.026; HBT, p = 0.011), β-nerve growth factor (HBT, p = 0.002; PDBT, p = 0.016), transforming growth factor-β1 (PDBT, p = 0.018; HBT, p < 0.004), brain-derived neurotrophic factor (PDBT, p = 0.011; HBT, p < 0.001) and fractalkine (PDBT, p = 0.045; HBT, p < 0.003) concentration only in training groups. In PDBT, we have found a significant decrease of tumor necrosis factor alpha. No training effect on concentration of interleukin6, insulin-like growth factor 1 and CD200 was observed in both training and control groups. Regular training can modulate level of inflammatory markers and induce neuroprotective mechanism to reduce the inflammatory response.