Neurorehabilitation courses employing a non-invasive brain-computer-hand exoskeleton interface in combination with traditional balneotherapy have been shown to reduce spasticity of hand muscles and improve motor skills in children with cerebral palsy. However, the coherence of the electroencephalogram (EEG) parameters have never been analyzed during such sessions. This study aimed to analyze the coherence changes in the bands of θ, α and β rhythms recorded in the EEG as part of balneotherapy combined with a course of neurorehabilitation prescribed to children with cerebral palsy, and to investigate the relationship of these changes with the indicators of motor activity. The study involved 23 children aged 7 through 15 years, both genders, diagnosed with spastic diplegia; we established coherence coefficients for the intra- and interhemispheric connections of the frontal, central, and parietal regions of the large hemispheres in the context of actions provoking kinesthetic imagery. A significant (p < 0.05) growth of the intrahemispheric connections coherence was registered for α rhythms, decline thereof — for θ, β1 rhythms, the fluctuations accompanied by a significant (p < 0.001) improvement of the motor functions on the Barthel scale. We identified a relationship between — rhythm coherence in the pair of C4–CP4 leads and the value of the Barthel index (r = 0.52; p = 0.04). The specifics of changes in the coherence of intrahemispheric connections within the studied rhythms can be used as indicators of neuroplasticity in children with cerebral palsy during rehabilitation, and support development of the new versions of the neurointerfaces classifier programs.