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Abstract Background Bedside teaching is a primary educational tool to improve the clinical practice of medical students. As a new medical pedagogical approach, team-based learning (TBL) is gradually being integrated into Chinese medical education programmes to promote clinical reasoning, knowledge application, teamwork and collaboration. The aim of this controlled study is to investigate the effects of TBL on pediatric bedside teaching in medical students. Methods Thirty medical students in pediatric clinical practice were randomly assigned to an intervention and a control group. Students in the intervention group exposed bedside teaching activity with TBL while students in the control group received traditional bedside teaching. Teaching for the two groups was conducted biweekly, and the same clinical cases were selected for both groups with the same instructors. After six months of clinical practice, the differences of learning outcomes between the two groups were compared through assessments by computer-based case simulations (CCS) and mini-Clinical Evaluation Exercise (mini-CEX). Student feedback following completion of bedside teaching was collected by questionnaire. Results The CCS scores in the intervention group were significantly higher than that in the control group (p