Stereochemistry is a vital component of pharmacy education, yet students often find it challenging due to the complex spatial concepts involved. This paper presents an innovative learning activity that combines inquiry-based learning with concrete molecular models to facilitate students’ understanding of stereochemistry. The activity was structured around a three-phase learning cycle, including exploration, concept invention, and application and was scaffolded by mini-lectures. Students in small groups constructed and analyzed 3D molecular models of organic compound isomers and formulated definitions and rules for different types of isomerism based on the exploration. Concrete models to visualize molecular structures reduced students’ cognitive load and provided kinesthetic and proprioception stimulation. Feedback from participating students indicated positive reception of the activity, highlighting the benefits of using concrete models and small group interactions. This innovative approach has demonstrated the potential of making stereochemistry more engaging and accessible for students.