Worldwide, young people’s interest in science, technology, engineering, and mathematics (STEM) education declines around pre-teen and early teenage years. Research shows that belief in one’s own scientific ability likely reinforces scientific ambition and effort, suggesting knowledge acquisition should not be neglected when encouraging scientific engagement. Educational tools harnessing three-dimensional (3D) visualisation technologies can increase engagement with science and facilitate knowledge acquisition, often proving more effective than traditional approaches. These educational tools prove particularly beneficial for anatomy education, as complex 3D structures and spatial relationships can be difficult to visualise and understand when learning from 2D materials. Hologram-based educational tools offer considerable advantages over 3D approaches such as virtual reality (VR), augmented reality (AR), and mixed reality (MR) as they do not require a head-mounted display or handheld equipment. Building upon previous research, this study presents a hologram-based application utilising a Pepper’s Ghost Illusion to educate young people on basic neuroanatomy, implementing gesture control paradigms via the Leap Motion Controller. User testing was conducted with twenty participants aged nine to twelve, assessing knowledge acquisition, usability, motivation, and cognitive load. The application significantly increased neuroanatomy knowledge by a mean of 30.25%, had a usability rating above the benchmark median, was motivating, and imposed low cognitive load. Limitations of this study include a lack of both participant demographic data and comparative data with traditional learning approaches. Applications of the type developed in this study represents a novel way/means of engaging young people with STEM education, in a manner potentially capable of combating their declining interest.