The enhancement of medical services relies significantly on engineering research. Magnetic actuation systems (MASs) are designed to be safe for biomedical applications and offer long‐distance and dynamic control capabilities, rendering them highly favorable for clinical applications. The integration of MASs with sophisticated perception and positioning methods enhances their suitability for clinical applications. Achieving this goal hinges on the development of MASs and their control methods; thus, a comprehensive review of current technical and scientific issues is indispensable for addressing the related challenges. This review encompasses both the classical and state‐of‐the‐art research, providing readers with a thorough understanding of the intricacies involved in MAS design, system control methods, clinical applications, and guidance toward the next phase of exploration. In addition, a detailed illustration of the underlying principles of the magnetic actuation method is provided, which helps delineate the design principles. A detailed analysis of potential clinical applications in hard‐to‐reach environments inside the human body provides guidance for interdisciplinary researchers. Challenges and opportunities associated with MAS design and application are summarized to inspire researchers and stimulate innovative explorations. Finally, this review concludes that sustained research in this field has the potential to yield groundbreaking advancements capable of revolutionizing modern medicine.