The magnetic navigation system (MNS) with gradient and uniform saddle coils is one of the effective systems to manipulate various medical magnetic robot due to its compact structure and uniformity of the magnetic field and field gradient. However, it has limited operating time and large inductance effect due to the high current density and numerous turns of coils, respectively. In this paper, we propose an optimization methodology of the MNS considering the current density and inductance of the coils. We introduce objective functions, constraints, and design variables of the MNS. Then, the MNS was designed by an optimization algorithm. The constructed MNS was compared with the conventional MNS, and it could generate 22 % stronger magnetic field or field gradient while the maximum three-dimensional rotating magnetic field was improved by 42 %. We also demonstrated an unclogging performance of a helical robot was improved by 54 % with the constructed MNS.