Chronic disease in a child, with the associated hospital stays, places considerable demands on the child and their family. The aim of this study was to investigate the parents’ perceptions of the music therapy used with their child during a hospital stay and to determine whether they felt that it reduced the child’s anxiety and stress generated by hospital admission. We hypothesized that the use of live music therapy from a music therapist would positively support these patients in everyday clinical practice, promote their wellbeing, and have positive impacts on their vital signs and blood pressure. Children with chronic gastroenterological and nephrological diseases included in this prospective study received live music therapy with a median duration of 41 min (range from 12 to 70 min) two to four times per week until discharged from the hospital. At the time of discharge, the parents were asked to complete a Likert-style questionnaire to evaluate the music therapy. Seven items were related to general questions about the patients and sessions, and eleven items evaluated the personal perceptions of the parents. Music therapy was conducted in 83 children, with a median age of 3 years (range from 1 month to 18 years). All parents (100%) completed the questionnaire at the time of discharge. Seventy-nine percent of the parents stated that their children were able to enjoy the music therapy sessions without being stressed. In addition, 98% of the respondents said that they were grateful for the music therapy their children received (97% fully agreed and 1% rather agreed). All parents considered music therapy to be beneficial for their child. The parents’ responses reflected the view that music therapy is beneficial to patients. According to the parents, music therapy can be integrated effectively in the inpatient clinical setting and can support children with chronic illnesses during their hospital stay.