This study estimated experimentally the loss distribution caused by magnetic friction in magnetic parts of a superconductor flywheel energy storage system (SFES) to obtain information for the design of high efficiency SFES. Through the spin down experiment using the manufactured vertical shaft type SFES with a journal type superconductor magnetic bearing (SMB), the coefficients of friction by the SMB, the stator core of permanent magnet synchronous motor/generator (PMSM/G), and the leakage flux of the metal parts were calculated. The coefficients of friction by the stator core of PMSM/G in case of using Si-steel and an amorphous core were calculated. The energy loss by magnetic friction in the stator core of PMSM/G was much larger than that in the other parts. The level of friction loss could be reduced dramatically using an amorphous core. Energy loss by the leakage magnetic field was small. On the other hand, the energy loss could be increased under other conditions according to the type of metal nearby the leakage magnetic fields. In manufactured SFES, the rotational loss by the amorphous core was approximately 2 times the loss of the superconductor and leakage. Moreover, the rotational loss by the Si-steel core is approximately 3~3.5 times the loss of superconductor and leakage.