The flipped classroom (FC) model has emerged as an innovative solution to improve student-centered learning. However, studies measuring student performance of material in the FC relative to the lecture classroom (LC) have shown mixed results. An aim of this study was to determine if the disparity in results of prior research is due to level of cognition (low or high) needed to perform well on the outcome, or course assessment. This study tested the hypothesis that (1) students in a FC would perform better than students in a LC on an assessment requiring higher cognition and (2) there would be no difference in performance for an assessment requiring lower cognition. To test this hypothesis the performance of 28 multiple choice anatomy items that were part of a final examination were compared between two classes of first year medical students at the University of Utah School of Medicine. Items were categorized as requiring knowledge (low cognition), application, or analysis (high cognition). Thirty hours of anatomy content was delivered in LC format to 101 students in 2013 and in FC format to 104 students in 2014. Mann Whitney tests indicated FC students performed better than LC students on analysis items, U = 4243.00, P = 0.030, r = 0.19, but there were no differences in performance between FC and LC students for knowledge, U = 5002.00, P = 0.720 or application, U = 4990.00, P = 0.700, items. The FC may benefit retention when students are expected to analyze material.