Indirect measurement of the flow rate of a centrifugal blood pump using the driving motor current was studied. The pump flow rate can be expressed as a function of the motor current under a given motor speed in the absence of energy loss resulting from uncertain mechanical contact friction. The magnetically suspended centrifugal blood pump (MSCP), developed by the collaboration of Kyoto University and NTN Inc., was suitable for the application of this measuring method because the impeller is suspended magnetically inside the pump housing without any mechanical contact. The effect of fluid viscosity on the pump performance was investigated in detail, and it was possible to estimate the pump flow rate and the pressure difference through the pump (from inlet port to outlet port) accurately by monitoring the motor current and speed when the kinematic viscosity of working fluids was known. The kinematic viscosity of working fluids can also be measured with the MSCP. The motor current and motor speed were monitored in a chronic animal experiment, and the estimated flow rate and pressure difference showed good correlation with directly measured data.