Human anatomy requires understanding spatial relationships among anatomical structures and is often perceived as difficult to learn by students. To overcome this concern, several digital tools exist with some strengths and limitations among which the lack of interactivity especially for complex functional anatomy learning. In this way, a new interactive three-dimensional tool called Antepulsio was designed. Antepulsio was assessed by comparing three groups of first year kinesiology students to test whether it is likely to favor functional anatomy learning during three training sessions spread over a week. The experiment was conducted during a real academic course. Laterality judgment, 3D spatial abilities and working memory abilities from all participants were previously collected to create three homogeneous groups: the active group (n = 17, 17.76 ± 0.56 years) interacted with Antepulsio, the passive group (n = 18, 17.89 ± 0.83 years) watched videos of Antepulsio while the control group (n = 15, 18.07 ± 0.80 years) performed a neutral activity unrelated to anatomy. Anatomy knowledge was also assessed during pretest, posttest, and retention test (8 weeks after the posttest). The most significant outcome of this study revealed that in case of better working visual memory, the active group outperformed the passive group between pretest and retention test (p < 0.01). In other words, Antepulsio tool is efficient only for students with high visuospatial working memory. These selective benefits of Antepulsio are discussed in terms of cognitive load, training duration and the necessary period of familiarization with the tool.