Background: Minutes after an injury to the spinal cord, structural and functional reorganization of the connected brain areas may be initiated. Exercise enhances this neuroplasticity in the further course of the condition, which might modulate the connectivity patterns in brain regions responsible for movement execution and imagination. However, connectivity patterns have not been analyzed as a correlate for activity effects on neuroplasticity after spinal cord injury (SCI). We hypothesize that wheelchair sport has a modulating effect on the cortical connectivity in patients with SCI, such that distinguished activity patterns can be observed between sportive and non-sportive individuals with SCI and healthy participants. Methods: Sportive (n = 16) and non-sportive (n = 7) patients with SCI as well as sportive (n = 16) and non-sportive (n = 14) healthy participants were instructed to either observe, imagine, or conduct an observed movement while high-density EEG (HD-EEG) was recorded. Functional connectivity was computed from the recorded signals, and the coefficients were compared between groups and conditions using a non-parametric repeated measures analysis. Results: We found that depending on being sportive or not, patients with SCI and controls would react differently to the conditions, but the effects depended on the location in the brain as well as the analyzed frequency range (p < 0.05). Further analysis indicates that non-sportive patients showed higher connectivity received by the right posterior parietal cortex and a lower connectivity received by the left M1 compared to sportive patients. These effects were mainly observed during movement imagination, not during movement. Sportive and non-sportive participants in the healthy control group showed smaller differences than the patients. Conclusions: The results suggest a modulative effect of sports on connectivity patterns during movement imagination and to some extent during movement. This effect was predominantly found in patients with SCI, and to a lesser extent in healthy participants with opposing connectivity patterns. We suggest that this might be due to increased cortical excitability and the elevated brain derived neurotrophic factor (BDNF) level in patients with SCI that is enhanced by exercise.