The navigated transcranial magnetic stimulation (nTMS)-based risk stratification was developed for patients with brain tumors in motor-eloquent location (compromising the motor cortex or the corticospinal tract [CST]) and has already been validated externally. The individual risk of a new or worsened motor deficit in the short term (on the day of discharge) and in the long term (3 months postoperatively) can be predicted based on the nTMS motor mapping and the nTMS-based tractography of the CST. A regression tree analysis is used to calculate the risk with the following three parameters: (1) infiltration of the motor cortex or CST (tumor-tract distance), (2) structural integrity of the CST (average fractional anisotropy) and (3) cortical excitability (resting motor threshold of the tumor hemisphere). Thus, patient counseling can be improved, and an individual treatment plan can be tailored by considering the potential risks and benefits.