Craniosynostosis is a rare and complex pathology, and visuospatial skills are necessary for a good understanding of the condition. While the use of three-dimensional (3D) models has improved the understanding of complex craniofacial anatomy, no study has evaluated the impact of this teaching support on long-term retention. Our randomized controlled trial was designed to compare the long-term retention of information with 3D-printed models of four types of craniosynostosis versus classic 3D reconstructions displayed in two-dimensional (2D) among undergraduate students. All students benefited from the same standardized course followed by the manipulation of the learning tool associated with the group for 15 min. Long-term retention was assessed by the capability to properly recognize different types of craniosynostosis 3 weeks after the course. Eighty-five students were enrolled. Previous educational achievements and baseline visuospatial skills were similar between the groups. The bivariate analysis showed the mean score in the 3D and 2D groups were 11.32 (2.89) and 8.08 (2.81), respectively (p < 0.0001). 3D-printed models of structures with spatial complexity such as various craniosynostosis patterns improve significantly medical students' long-term retention, indicating their educational efficacy.