Background: Several studies have reported contradictory results regarding the benefits of music interventions in children and adolescents with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). Methods: We performed a systematic review according to the PRISMA guidelines. We searched the Cochrane, PubMed and Medline databases from January 1970 to September 2020 to review all empirical findings, except case reports, measuring the effect of music therapy on youths with ASD, intellectual disability (ID), communication disorder (CD), developmental coordination disorder (DCD), specific learning disorder, and attention/deficit hyperactivity disorder (ADHD). Results: Thirty-nine studies (N = 1,774 participants) were included in this review (ASD: n = 22; ID: n = 7; CD and dyslexia: n = 5; DCD: n = 0; ADHD: n = 5 studies). Two main music therapies were used: educational music therapy and improvisational music therapy. A positive effect of educational music therapy on patients with ASD was reported in most controlled studies (6/7), particularly in terms of speech production. A positive effect of improvisational music therapy was reported in most controlled studies (6/8), particularly in terms of social functioning. The subgroup of patients with both ASD and ID had a higher response rate. Data are lacking for children with other NDDs, although preliminary evidence appears encouraging for educational music therapy in children with dyslexia. Discussion: Improvisational music therapy in children with NDDs appears relevant for individuals with both ASD and ID. More research should be encouraged to explore whether oral and written language skills may improve after educational music therapy, as preliminary data are encouraging.