A superconducting(SC) magnetically levitated (Maglev) transportation system has been developed in Japan and various experiments have been done in the new test line at Yamanashi prefecture. Although the superconducting electrodynamic suspension (EDS) system has the advantage of stable levitation without active control, various electromagnetic or mechanical disturbances can cause the change of gap length and the displacement or oscillation of the bogie. As the damping of the EDS system is shown to be small, additional damping factor is needed to increase the stability of the levitation under the influence of disturbance. Then the damper coil system is proposed. The copper coils are installed in front of the SC coils on the bogie. We have developed three dimensional numerical simulation program for the Maglev bogie. The damper coils system is included in this program, and running simulations of the Maglev bogie are undertaken. The damping factor for each rotational direction is shown. The running simulation when the bogie passes the lateral guideway displacement is calculated, and effect of the damper coils is clearly shown.