BACKGROUND: In the face of challenging anatomy and rigidly designed medical school schedules, student learning and well-being is under threat. It is high time to tap into innovative strategies like clay-based learning (CBL) to counter financial or infrastructural limitations in order to improve student experiences with learning neuroanatomy and simultaneously offer a therapeutic outlet. APPROACH: We followed a two-phased approach starting with conception to execution. Session components were defined, and the activity was carried out in pairs. Students used play-dough and simple tools to construct a model of the brainstem, selected due to its structural and relational complexity. A reflective assessment task was also included as part of the session to meta-physically engage the students. EVALUATION: Students shared detailed feedback about the session and also participated in a formative MCQ-based test. These were analysed quantitatively and qualitatively under our multifaceted approach to evaluation allowing us to explore the value of CBL beyond its role as an active learning tool. IMPLICATIONS: Student experiences have far-reaching consequences that potentially impact not only their learning but also mental well-being. Attempts to rectify or improve them should be undertaken thoughtfully to ensure that intended aims are being accomplished adequately. CBL is a strategic tool that can repair student engagement with challenging subjects like neuroanatomy especially when incorporated in ways that account for student perspectives.