The present study is set out to systematically investigate the combined impact of operational, geometrical, and model uncertainties on the hemodynamics and performance characteristics in the US Food and Drug Administration (FDA) benchmark centrifugal blood pump. Non-intrusive Polynomial Chaos Expansion (NIPCE) has been utilized to propagate the uncertainty of 12 random input variables in the flow field and the performance characteristics of the blood pump at three working conditions. The global sensitivity of the Quantities of Interest (QoI) to the uncertain input parameters was measured through the Sobol’indices. The Multiple Reference Frames (MRF) approach and the SST k− ω turbulence model were employed to conduct the 3D CFD computations of the pump. In addition, we quantified the device-related hemolysis using the semi-empirical power-law model. The stochastic CFD results of the pump velocity field and hydraulic performance parameters showed a satisfactory agreement with measurements. Statistical analysis indicated that the effect of operational and geometrical uncertainties on the velocity field of the blood pump chiefly emerges at the outlet diffuser region, more specifically along the center-line of the fluid jet formed inside the diffuser. This study has also clarified that the uncertainties in the flow field and the hydraulic performance of the blood pump are mainly due to the variations of impeller diameter, rotational speed, radial clearance, and flow rate. By contrast, the hemolysis index is profoundly affected by the model parameters. Additionally, higher robustness against uncertainties was observed for hydraulic efficiency compared to the pump head. Eventually, it was shown that the maximum value of the distribution function of the relative hemolysis index lies within the bounds of the measurements.