Background and Objectives: Children with developmental coordination disorder (DCD) have difficulty learning motor skills, which can affect their participation in activities of daily living and psychosocial well-being. Over 50% of children with DCD also have attention deficit hyperactivity disorder (ADHD), which further exacerbates their motor problems and impact on quality of life. A rehabilitation approach known as Cognitive Orientation to Occupational Performance uses problem-solving strategies to help children learn motor skills they wish to achieve. While this cognitive approach has been effective for children with DCD, few studies have examined the effectiveness of this approach for children with co-occurring ADHD. Further, the underlying mechanism and neural basis of this intervention are largely unknown.Methods: In this randomized waitlist-controlled trial, we used MRI to examine white matter microstructure after intervention in 8–12-year-old children with DCD (n = 28) and with DCD and co-occurring ADHD (n = 25). Children in both groups were randomized to either a treatment group or waitlist group at their first MRI. The treatment group began the intervention after their MRI scan and returned for a post-treatment scan at 3 months, and follow-up scan at 6 months; the waitlist group waited 3 months before their second MRI, received the intervention, and then had a post-treatment scan. Each child received intervention once weekly for 10 weeks. Diffusion tensor imaging was used to acquire white matter diffusion parameters and was analyzed using tract-based spatial statistics (TBSS).Results and Conclusion: Children with DCD showed significant improvement in white matter microstructure in the bilateral anterior thalamic radiation, bilateral sensorimotor tract, bilateral cingulum, fornix, splenium and body of corpus callosum, right inferior fronto-occipital fasciculus, and white matter pathways to bilateral inferior gyri, right middle frontal gyrus, frontal medial cortex, and left cuneus. We suggest that these rehabilitation-induced neural changes in children with DCD occurred in regions associated with attention, self-regulation, motor planning, and inter-hemispheric communication, which positively affected brain connectivity and motor function. In contrast, children with DCD and co-occurring ADHD did not show any brain changes following the intervention. Modifications to the treatment protocol might help address the attentional and self-regulatory needs of children with a dual diagnosis.Clinical Trial Registration: ClinicalTrials.gov ID: NCT02597751.