Flipped classrooms are being utilized more frequently in biomedical education to provide more active learning opportunities to students although there are mixed results on the benefits of the flipped classroom in biomedical education. In this study, the effects of using a flipped classroom with case-based learning in the endocrine section of a first-year veterinary-integrated histology and physiology course were investigated. Results demonstrated that the flipped classroom improved performance on the endocrine section exam by 15.9% (Cohen's d = 1.08; P < 0.001) with improvements on both clinically applicable and basic knowledge questions. Student satisfaction with the flipped classroom was also investigated. Students reported high satisfaction with the in-class case-based learning opportunities but lower satisfaction with the asynchronous content delivery and the time required outside of class. Student perceptions of the flipped classroom were measured again after being exposed to the results of the flipped classroom on student learning. After seeing the results, students were significantly more likely to value the time spent in the flipped classroom and to desire more opportunities for flipped classrooms in the future.