The superconducting synchronous motor or generator mostly has high permeability iron only around outer yoke portion. Therefore, if excitation voltage (Back E.M.F) is calculated from 2 dimensional magnetic field distributions, it can be largely different from actual value due to additional voltage originated from end coils. In order to calculate the excitation voltage more accurately, 3 dimensional magnetic field calculation is necessary for including the end coil effect from large air-gap structure. The excitation voltage can be calculated by stator (armature) coil linkage flux originated from rotor (field) coil excitation, but it is difficult to calculate the flux linkage exactly because of complicated structure of the stator coil. This paper shows a method to calculate the excitation voltage from 3 dimensional magnetic energy that can be calculated directly from volume integration of magnetic flux density and field intensity scalar product through FEM (Finite Element Method) analysis software.