Studies of motor outcome after Neonatal Arterial Ischemic Stroke (NAIS) often rely on lesion mapping using MRI. However, clinical measurements indicate that motor deficit can be different than what would solely be anticipated by the lesion extent and location. Because, this may be explained by the cortical disconnections between motor areas due to necrosis following the stroke, the investigation of motor network can help in the understanding of this discrepancy between visual inspection and outcome. In this study, we propose to examine the structural connectivity between motor areas in NAIS patients in comparison to healthy controls in order to define the cortical and subcortical connections that are can depict motor outcome. Accordingly, 30 healthy controls and 32 NAIS patients with and without Cerebral Palsy (CP) underwent MRI acquisition and manual assessment. The connectome of all participants was obtained from T1-weigted and diffusion weighted imaging. Results showed significant disconnections in the lesioned as well as the contra-lesioned hemisphere of patients. Furthermore, significant correlations were found between the structural connectivity metric of specific motor areas and manuality assessed by the Box and Block Test (BBT) scores in patients. Using the connectivity measures of these links we were able to estimate the BBT score using a multiple linear regression model. Based on one connection value we were also able to predict the presence or not of CP. According to our results, structural connectome, can be an asset in the estimation of gross manual dexterity after neonatal stroke.