The study investigated the effectiveness of a flipped classroom (FC) combined with case-based learning (CBL) in 115 undergraduate medical students during a pediatric clinical rotation. The students were randomly divided into an intervention group (FC + CBL) and a control group with traditional lecture teaching. The intervention group scored significantly higher in overall assessment, theoretical knowledge and objective structured clinical examination (OSCE) than the control group (p < 0.05), but the difference was not significant in routine performance. In the subjective evaluation, the intervention group scored significantly higher in active learning, critical thinking, learning effectiveness, teamwork, communication, problem solving, skill training, motivation, and overall effectiveness (p < 0.01). Correlation analysis showed stronger positive associations between active learning, critical thinking, motivation and objective outcomes in the intervention group. The conclusion of the study confirms that FC + CBL improves both objective results and subjective experiences in pediatric clinical training.