Introduction Teaching of human anatomy has undergone significant changes in the past three decades. At the University of Rwanda, anatomy is being taught using team-based learning (TBL). While student-generated multiple choice questions (MCQs) stimulate deeper thinking on a given topic, their impact on anatomy learning is not known. This study aimed to find out the impact of student-generated MCQs on the current anatomy teaching method at the University of Rwanda. Methods In this comparative interventional study, two similar chapters on anatomy were selected; one was taught using TBL while for the other one, in addition to TBL, students were encouraged to set MCQs while studying. Pre- and post-test scores were analyzed using SPSS 23 and the Student’s t -test was used to compare the mean scores obtained. Results Thirty-one medical students were recruited. Pre-test mean scores were 25.10 and 25.19 out of 50 for chapters 1 and 2, respectively. Although the students’ post-test scores improved after teaching for each chapter, the improvement was much greater for chapter 2 than for chapter 1, with mean scores of 39.97 and 32.45 out of 50, respectively ( P <0.05). Despite such improvement, almost half of the students found that setting MCQs was not easy. Conclusion This study found that student-generated MCQs can be used as a simple and cost-effective tool to enhance TBL of anatomy.