Motor coordination abilities are related to cognitive abilities and academic achievement in children with neurodevelopmental disorders. However, the similarities and differences of these relationships in children with autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (AD/HD) have not been explored. The purpose of this study was to investigate the relationship between motor coordination abilities, cognitive abilities, and academic achievement in Japanese children with ASD and AD/HD. Participants included 20 children with ASD, 20 children with AD/HD, and 20 typically developing children, matched for age and gender. Their motor coordination abilities were assessed with the Movement Assessment Battery for Children-2 (MABC-2). Furthermore, cognitive ability and academic achievement were assessed with the Kauffman Assessment Battery for Children-II (K-ABCII). Results demonstrated that the MABC-2 Total score significantly correlated with the K-ABCII Simultaneous processing, Planning, Total cognitive ability, Writing and Arithmetic scores in children with ASD. However, in children with AD/HD, there was no significant correlation between MABC-2 and K-ABCII subscale scores. The results of this study indicated that the relationship between motor coordination ability, cognitive ability, and academic achievement differs between ASD and AD/HD. This difference might indicate the non-similarity of neurological characteristics and encourage consideration for an approach that accommodates the features of neurodevelopmental disorders in children.