Magnetic navigation systems are used to precisely manipulate magnetically responsive materials enabling the realization of new minimally invasive procedures using magnetic medical devices. Their widespread applicability has been constrained by high infrastructure demands and costs. we report on a portable electromagnetic navigation system, the Navion, which is capable of generating a large magnetic field over a large workspace. The system is easy to install in hospital operating rooms and transportable through healthcare facilities, aiding in the widespread adoption of magnetically responsive medical devices. First, we introduce our design and implementation approach for the system and characterize its performance. Next, we demonstrate in vitro navigation of different microrobot structures using magnetic field gradients and rotating magnetic fields. Spherical permanent magnets, electroplated cylindrical microrobots, microparticle swarms, and magnetic composite bacteria‐inspired helical structures are investigated. we also demonstrate the navigation of magnetic catheters in two challenging endovascular tasks: (1) an angiography procedure and (2) deep navigation within the circle of Willis. Catheter navigation is demonstrated in a porcine model in vivo to perform an angiography under magnetic guidance.This article is protected by copyright. All rights reserved