Highlights•The nTMS model with its functional data and nTMS-based tractography was superior to the clinicoradiological PrS model for predicting motor outcome in motor eloquent brain tumor resection.•The cortical nTMS mapping, the tumor-tract distance, the white matter integrity and the cortical excitability were integrated into a regression tree analysis to predict the short- and longterm motor outcome.•A combined model has been developed to predict the EOR most accurately using parameters from both models.•Patients with motor-eloquent brain tumors should be treated in large centers with expertise in nTMS and tractography to achieve the optimal functional outcome and extent of resection.