Neuroanatomy is often considered a difficult subject to teach, due to its broad scope, multitude of terms, and high degree of complexity. Thus, newer educational strategies that facilitate learning while also stimulating students by allowing increased student autonomy and group discussions should be carefully considered. This study aimed to evaluate the impact of introducing team-based learning (TBL) in the traditional discipline of neuroanatomy and to measure student knowledge acquisition and perception relative to traditional lectures (TL). A quasi-experimental, nonrandomized study was performed using two consecutive TBL classes (intervention group, n = 157 students, 25% content using TBL) with a TL class (control group, n = 76). Team-based learning sessions included all stages according to the classic description of the method. Student knowledge acquisition was assessed in regularly scheduled tests during the discipline, and their perception regarding TBL was evaluated using a questionnaire (developed by the authors). The groups presented a similar sociodemographic profile (sex and age) and the same performance in another anatomy discipline before the study. Team-based learning was significantly associated with greater acceptance, higher motivation, better student perception, and feelings that the methodology was able to integrate clinical and basic sciences. Nevertheless, according to tests, knowledge acquisition was similar between the TBL and lectures. In conclusion, since TBL is comparable to TL for knowledge acquisition, TBL seems to be a promising strategy to improve the teaching of neuroanatomy in medical schools. It fosters group discussions and increases satisfaction and the perception of integration between clinical and basic sciences.