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The hemocompatible properties of rotary blood pumps commonly used in mechanical circulatory support (MCS) are widely unknown regarding specific biocompatibility profiles of different pump technologies. Therefore, we analyzed the hemocompatibility indicating markers of an axial flow and a magnetically levitated centrifugal device within an in vitro mock loop. The HeartMate II (HM II; n = 3) device and a CentriMag (CM; n = 3) adult pump were investigated in a human whole blood mock loop for 360 min using the MCS devices as a driving component. Blood samples were analyzed by enzyme-linked immunosorbent assay for markers of coagulation, complement system, and inflammatory response. There was a time-dependent activation of the coagulation (thrombin–antithrombin complexes [TAT]), complement (SC5b-9), and inflammation system (polymorphonuclear [PMN] elastase) in both groups. The mean value of TAT (CM: 4.0 μg/L vs. 29.4 μg/L, P < 0.001; HM II: 4.5 μg/L vs. 232.2 μg/L, P < 0.05) and PMN elastase (CM: 53.4 ng/mL vs. 253.8 ng/mL, P < 0.05; HM II: 28.0 ng/mL vs. 738.8 ng/mL, P < 0.001) significantly increased from baseline until the end of the experiments (360 min). After 360 min, TAT and PMN values were significantly higher in the HM II group compared with the values in the CM adult group. The values of SC5b-9 increased from baseline to 360 min in the CM group (CM: 141.8 ng/mL vs. 967.9 ng/mL, P < 0.05) and the HM II group. However, the increase within the HM II group (97.3 vs. 2462.0, P = 0.06) and the comparison of the 360-min values between CM group and HM II group did not reach significance (P = 0.18). The activation of complement, coagulation, and inflammation system showed a time-dependent manner in both devices. The centrifugal CM device showed significantly lower activation of coagulation and inflammation than that of the HM II axial flow pump. Both HM II and CM have demonstrated an acceptable hemocompatibility profile in patients. However, there is a great opportunity to gain a clinical benefit by developing techniques to lower the blood surface interaction within both pump technologies and a magnetically levitated centrifugal pump design might be superior.