Electroencephalography (EEG) studies have shown that the experience of social interaction in interpersonal relationships may be reflected physiologically in brainwave synchronization. However, how music engages the neuro-mechanisms of empathy in children with developmental disabilities is not known. Therefore, this hyperscanning case study investigated brain synchronization between two dyads (child –parent, child -music therapist). Four children with disabilities (e.g. cerebral palsy, autism spectrum disorder) attended 3 music and 3 storytelling sessions (20 min. each). The parent observed the session via a screen which was not visible to the child and therapist. The strength and directionality of brainwave synchronizations for two dyads were recorded simultaneously. The results indicated that music sessions (M = .16, SD = .05) showed significantly higher coherence compared to storytelling sessions (M = .13, SD = .04), p = .05. Moreover, the coherence in delta frequency band was significantly higher than other frequency bands (p < .001) in child-parent dyad. Interestingly, the directionality from adult (parent or therapist) to child participants yielded significantly higher synchronization compared to child to adult directionality. Findings show the emergence of potential physiological signatures of social interaction during neurologic music therapy between parent and therapist towards the child.