Minimally invasive surgery (MIS) has become increasingly favored by both patients and surgeons owing to its advantages such as shortened recovery times and reduced surgical trauma. To enhance intraoperative feedback from surgical instruments while minimizing harmful radiation exposure, a wide range of electromagnetic tracking systems (EMTS) has been developed at micro scales for medical applications. This review provides a comprehensive summary of advances in the field over the past five years, with an emphasis on the working principles of EMTS, system architecture, current research progress, and clinical applications. In comparison to other review papers, this article focuses specifically on EMTS for medical micro-devices, such as robotic catheters, endoscopes, and capsule robots. Moreover, Representative research studies and commercial systems are presented along with their clinical implementations, placing greater emphasis on the translation of EMTS into medical applications. Finally, this review outlines and discusses future research directions, highlighting major challenges and potential opportunities for advancing the integration of EMTS into routine clinical workflows.