In this paper, the rotational loss of the superconductor flywheel energy storage system (SFES) by motor/generator stator core was assessed. To do this, the vertical axial type SFES with journal type superconductor bearing was manufactured. To quantitatively assess the rotational loss by the stator core, the rotational losses by superconductor bearing and the degree of a vacuum were measured. In case of variation of the inner radius and outer radius of the stator core, the rotational losses were measured. From the experimental results, It is confirmed that the rotational loss can be reduced by means of the optimal stator core design.