Augmented Reality (AR) is increasingly used as an educational tool in a range of domains with the goal of enhancing students’ performance as well as their learning experience, thanks to the interactivity and visual appeal of AR objects. While some attempts, albeit limited, have been undertaken to prove these beneficial effects in learning 3D geometry, the results remain inconclusive and there are some methodological issues such as under-evaluation of user experience. With the aim to enrich the applied body of knowledge on this specific topic, we developed an AR application that allows its users to learn about cross-sectional shapes and variables in 3D geometry. We compared the AR-based approach with the traditional chalk-and-board approach by involving sixty 12–16 year-olds from two schools. The AR class showed a significantly stronger learning effect than the traditional class, especially for the more complex geometric concepts. The AR class found the application engaging, regardless of their level of knowledge gain, which bore no significant relation with their intention to use it. The methodological challenge for implementing control groups and the practical challenge for affordable emerging educational tools should be tackled in future research.