Purpose: Three-dimensional (3D)–printed models have been increasingly used in medical education, but most studies have focused on satisfaction or outcomes following isolated learning activities. This study aimed to explore students’ perceptions of learning, engagement, usability, and learning strategies after completing a series of neuroanatomy-related coloring activities using a low-cost 3D-printed model. Methods: This cross-sectional study involved Year 1 medical students at Duke-NUS Medical School. Students participated in 3 structured coloring activities using a modular 3D-printed brain model during a neuroanatomy session. An anonymous survey was administered 1 week after the third activity to assess students’ perceived learning value, engagement (behavioral, cognitive, emotional, and agentic), usability, and learning strategies using Likert-scale items and open-ended questions. Results: A total of 48 students completed the survey, and the instrument showed acceptable to high internal consistency. Students reported high perceived learning value, positive engagement across multiple domains during the coloring activity, and high usability of the model. Participation in the learning activities was associated with significantly higher behavioral and agentic engagement, perceived learning value, and greater use of learning strategies than non-participation. Overall, active manipulation and hands-on exploration were perceived as beneficial for learning. Conclusion Low-cost 3D-printed brain models may serve as valuable learning tools to complement existing anatomy teaching approaches when paired with well-designed learning activities. Students reported positive learning experiences and high engagement during the activities. These findings highlight the importance of sound pedagogical design and curriculum integration to maximize learning.