Science, magic, and education have always been linked, from science-based magic shows to teachers presenting demonstrations as magic tricks to capture their students’ interest and provide a mnemonic reference for the topics under discussion. Magic as an art form is also often used to convey information or act as an analogy for invisible phenomena. This study examined how the use of a magic effect designed as an analogy for active and passive transport in cells affected student scores and perception of the activity when compared to a standard story analogy in a high school integrated science course. To determine this, students participated in either a magic-based analogy activity (MBAA) or a concrete story-based analogy activity (SBAA), and then data was collected and analysed using a pre-test/post-test for the content and a Likert-scale anonymous survey for the student perception of the activity. The MBAA was shown to be similar to the SBAA in helping students learn but had the added benefit of increasing students’ reported engagement with the activity. This study shows how bringing magic into the science classroom can have a positive impact on student engagement and provides teachers with another option to support student learning.