Preoperative brain mapping is vital to improve the outcome of patients with tumors located in eloquent areas. While functional magnetic resonance imaging (fMRI) remains the most commonly used preoperative mapping technique, navigated transcranial magnetic stimulation (nTMS) has recently been proposed as a new preoperative method for the clinical and surgical management of such patients. This study aims at evaluating the impact of nTMS as a routine examination and its ultimate contribution to patient outcome. We performed a preliminary prospective study on eight patients harboring a cerebral lesion in eloquent motor areas. Each patient underwent preoperative cortical brain mapping via both fMRI and nTMS; then, we assessed the reliability of both methods by comparing them with intraoperative mapping by direct cortical stimulation (DCS). This study suggests that nTMS was more accurate than fMRI in detecting the true cortical motor area when compared with DCS data, with a mean of deviation ± confidence interval (CI) of 8.47 ± 4.6 mm between nTMS and DCS and of 12.9 ± 5.7 mm between fMRI and DCS (p < 0.05). The results indicated that within the limits of our statistical sample, nTMS was found to be a useful, reliable, and non-invasive option for preoperative planning as well as for the identification of the motor strip; in addition, it usually has short processing times and is very well tolerated by patients, thereby increasing their compliance and possibly improving surgical outcome.