Background Team-Based Learning methodology (TBL) is used in medicine teaching in different clinical and basic fields, but seldom in statistics courses. Aim To compare the performance of students taught using TBL with those receiving the traditional lecture modality. Materials and Methods The grades and percentage of correct answers obtained in exams written during the statistics course of students that were taught without TBL (years 2009-2011) or using this methodology (years 2013-2016) were compared. Z Test for one mean (Milestone 1) and Student's t test for two independent means assuming equal variances/unequal variances (Milestone 2) were evaluated. The mean and minimum grades and the percentage of grades below the flunking threshold were also evaluated. Students' assessment of the methodology was also recorded. Results The percentage of correct answers was 94.2% and 94% among students taught with and without TBL methodology, respectively (Milestone 1), achieving a similar performance independent of the teaching strategy. The global percentage of correct answers of Milestone 2 increased from 75.3% to 89.5% (P < 0.001) among students using TBL. In 75.0% of questions, the percentage of correct answers increased with TBL. Likewise, there was an increase in mean grades increased from 5.4 to 6.2 (P < 0.05) and mean minimum grades from 2.8 to 3.7 (P = 0.05). The proportion of grades below the flunking threshold decreased from 9.9% to 4.4% (P = 0.054). Almost all students evaluated TBL methodology positively. Conclusions Students taught using TBL methodology performed better in the statistics course evaluation than students attending standard lectures in statistical analysis of greater complexity. TBL was well evaluated.