The complexity of modern societies necessitates that children learn highly abstract material, such as mathematics, which often conflicts with behavioral goals that are innately motivating. For instance, children's educational success is generally evaluated based on their individual achievements, while humans are motivated to learn by engaging in socially relevant behaviors. Additionally, science-related content typically requires higher-level abstract thinking to comprehend related concepts and perform the underlying cognitive processes, whereas humans evolved primarily to monitor and manipulate the physical environment by moving within it to execute foraging and hunting behaviors. Moreover, school systems inherently prescribe top-down strategies in which teachers transfer knowledge by providing instructions to guide students' knowledge acquisition. By contrast, humans evolved to learn through bottom-up processes motivated by the learner's internal drive to explore their physical and social environment. As a consequence, skeletal cognitive competencies that evolved throughout human history create a mismatch between why children are motivated to learn and how they are expected to learn. This review adopts an evolutionary perspective to examine how the interplay between students' internal physiological and psychological adaptations and external instructional methods of modern educational systems impacts motivation and learning. Ultimately, the review offers suggestions on how to motivate the learning process by integrating self-determination theory principles into a dynamical systems framework.