One of the major challenges facing anatomy educators is delivering the anatomy materials in fewer hours with a reduction of anatomy courses in the integrated curricula. The flipped classroom modality may be an innovative solution. However, its effectiveness remains under debate due to a lack of outcome-based research and the mixed results of students' performance. The present study aimed to determine the outcome of the flipped classroom based upon the level of student cognition. The study investigated performance on 17 multiple-choice anatomy questions as a part of the final examination of the musculoskeletal system module. The results were compared between the first-year female students of Qassim Medical College, specifically the flipped classroom group (46 students) of the academic year (2018-2019) and the traditional group (49 students) of the academic year (2017-2018). The mean differences in the students' grades on the anatomy questions at the level of knowledge, application, and analysis using Cohen's d test were 0.43, 1.41, and 1.01, respectively. These results suggest the positive impact of flipping the students' classrooms on improving their levels of thinking according to Bloom's taxonomy. Perception surveys also revealed students' enthusiasm for the pre-class activities, leading to a better performance in the class with more engagement with their peers and teachers. The present study suggested that the flipped classroom modality can be performed to compensate for the reduction of anatomy educational hours. However, further studies are recommended to investigate the best practices of the flipped classroom that fit with the students' needs and workloads.