Although embryology lays a strong foundation for understanding gross anatomy, variations, and congenital anomalies, its educational contact hours in the North American medical curricula have become minimal and integrated with other subjects. This poses challenges for students to learn the spatially complex developmental processes, leading many to seek external online resources or resort to rote memorization for the short‐term, neither an ideal solution.To promote effective learning and retention, embryology curriculum was offered in a flipped‐class format in the Fall of 2019 for first‐year medical students. Eleven, 8–16 minute tutorial videos were produced for each hour of embryology lecture in the integrated anatomy course. Before each embryology lecture, students were required to view the tutorial and complete a quiz. The lectures were customized based on pre‐lecture quiz outcomes and in‐class poll to review the difficult concepts, to solve clinical cases, and to complete additional assessments. Before each test in the course, students completed 2 additional hours of active learning sessions, which provided a variety of resources, including more clinical cases, assessment‐based learning, and various visual and physical embryo models. In an IRB‐exempt (#19‐1716), retrospective study, students’ embryology exam performances from the flipped class curriculum were compared with the previous year’s data (2018). The 2018 cohort received nearly identical educational materials, including the learning objectives, active learning sessions, and assessments, but lectures were provided in didactic presentations. The embryology instructor was the same individual in 2018 and 2019.Embryology exam data were analyzed using Item Response Theory, controlled for item difficulty differences. The results reveal that the 2019, flipped‐class cohort (n=184) had higher embryology exam performances in all 4 exams than the 2018, didactic cohort (n=184). T‐Tests revealed that the 2019 cohort performed significantly higher than the 2018 counterparts on embryology in the 2nd exam (p<0.01) and the comprehensive final (p<0.05). Interestingly, in student evaluations, the same embryology instructor was rated significantly lower on educational effectiveness by the 2019 cohort compared to the 2018 cohort. Thematic analysis of the evaluation comments revealed that though 2019 students found the instructor likable and appreciated the resources, efforts, and enthusiasm, the overwhelming majority disliked the flipped classroom model, citing that it did not help them learn, caused more confusion, and lectures felt disorganized.The learning outcomes of this study are consistent with the literature indicating the effectiveness of the flipped classroom in student learning and engagement; however, the negative outcomes of the educator evaluation is alarming and points to the importance of student education about evidence‐based pedagogical practices and student buy‐in.