Objectives: This study examined microstructural properties of cortical and subcortical gray matter components of the dorsolateral prefrontal (DLPFC) cortical-subcortical circuit in relation to parent-rated executive function and fine motor dexterity performance in youth with spina bifida myelomeningocele (SBM). Aberrant gray matter integrity of the DLPFC, basal ganglia nuclei, and thalamus were hypothesized to differentially relate to neurobehavioral outcomes. Methods: Forty-nine youth between 8 and 18 years (M = 12.34) old with SBM underwent a 3T MRI including diffusion tensor imaging. Neurobehavioral measures of parent-rated executive function and fine motor dexterity were obtained from a standardized neuropsychological evaluation. Relations among indices of gray matter microstructural integrity (mean diffusivity [MD], fractional anisotropy [FA], cortical thickness) and neurobehavior were examined using 3 correlational methods to enhance reliability of brain-behavior relations. Results: In SBM, higher FA values in the caudate were associated with poorer behavioral regulation. Higher FA values in the putamen and greater DLPFC thickness were both associated with poorer fine motor dexterity. Conclusion: Behavioral regulation and FA in the caudate related to behavioral inhibition in SBM. Similarly, associations between fine motor dexterity and indices of gray matter integrity in the putamen and DLPFC support fronto-striatal involvement in motor control in SBM. Examination of these neurobehavioral correlates revealed a pattern of attenuated behavioral impairments when gray matter structure was more similar to that of typically developing youth.