Recently, the locomotion of a microrobot wirelessly actuated by electromagnetic actuation systems has been studied in many ways. Because of the inherent characteristics of an electromagnetic field, however, the magnetic field of each coil in the electromagnetic actuation system induces magnetic field interferences, which can distort the desired electromagnetic field, preventing the microrobot from following the desired path. In this article, we used two pairs of Helmholtz coils and two pairs of Maxwell coils in a two-dimensional electromagnetic actuation system. Generally, the two pairs of Helmholtz coils generate the torque for the rotation of the microrobot and the two pairs of Maxwell coils generate the propulsion force of the microrobot. Both pairs of Helmholtz and Maxwell coils have to work to simultaneously align and propel the microrobot in a desired direction. In this situation, however, the electromagnetic fields produced by the Helmholtz coils can interfere with those produced by the Maxwell coils. This interference is closely dependent on the position of the microrobot in the region of interest inside the electromagnetic coils system. This means that the alignment direction and propulsion force of the microrobot can be distorted according to the position of the microrobot. Therefore, we propose a compensation algorithm for the electromagnetic field interference using the position information of the microrobot to correct the magnetic field interferences. First, the interference of an electromagnetic field obeying the Biot–Savart law is analyzed by numerical analysis. Second, a position-based compensation algorithm for the locomotion of a microrobot is proposed. Various locomotion tests of a microrobot verified that the proposed compensation algorithm could reduce the normalized average tracking error from 5.25% to 1.92%.