Children with Developmental Coordination Disorder (DCD) are characterized as having motor difficulties and learning impairment that may last well into adolescence and adulthood. Although behavioral deficits have been identified in many domains such as visuo-spatial processing, kinesthetic perception, and cross-modal sensory integration, recent studies suggested that the functional impairment of certain brain areas, such as cerebellum and basal ganglia, are the underlying causes of DCD. This review focuses on the "motor learning deficits" in DCD and their possible neural correlates. It presents recent evidence from both behavioral and neuroimaging studies and discusses dominant neural hypotheses in DCD. Given the heterogeneity of this disorder, a successful intervention program should target the specific deficits on an individual basis. Future neuroimaging studies are critical steps in enhancing our understanding of learning deficits in DCD.