The pterygopalatine fossa (PPF) is a bilateral space deep within the skull that serves as a major neurovascular junction. However, its small volume and poor accessibility make it a difficult space to comprehend using two-dimensional illustrations and cadaveric dissections. A three-dimensional (3D) printed model of the PPF was developed as a visual and kinesthetic learning tool for completely visualizing the fossa, its boundaries, its communicating channels, and its neurovascular structures. The model was evaluated by analyzing student performance on pre- and post-quizzes and a student satisfaction survey based on the five-point Likert scale. The first cohort comprised of 88 students who had never before studied the PPF. The second cohort consisted of 30 students who were previously taught the PPF. Each cohort was randomly divided into a control group who were provided with a half skull and an intervention group that were provided with the 3D printed model. The intervention group performed significantly better on the post-quiz as compared to the control group in cohort I (P = 0.001); while not significant, it also improved learning in cohort II students (P = 0.124). Satisfaction surveys indicated that the intervention group found the 3D printed model to be significantly more useful (P < 0.05) as compared to the half skull used by the control group. Importantly, the effect sizes for cohorts I and II (0.504 and 0.581, respectively) validated the statistical results. Together, this study highlights the importance of 3D printed models as teaching tools in anatomy education.