Although experimental extracorporeal membrane oxygenation (ECMO) animal models have been reported, there are few studies on the immune response to ECMO. We developed the venoarterial (VA) and venovenous (VV) model in rats and serially investigated the changes in the distribution of immune cells. Forty rats underwent both VA and VV modes of ECMO, and blood samples were collected at 1 day before ECMO (D-1), at the end of ECMO run (D+0), and 3 days after the ECMO (D+3). Flow cytometry was used to characterize surface marker expression (CD3, CD4, CD8, CD43, CD45, CD45R, CD161, and His48) on immune cells. Granulocytes were initially activated in both ECMO types and were further reduced but not normalized until 3 days of decannulation. Monocyte and natural killer cells were decreased initially in VA mode. B lymphocytes, helper T lymphocytes, and cytotoxic T lymphocytes also significantly decreased in VA modes after ECMO, but this phenomenon was not prominent in the VV modes. Overall immune cells proportion changed after ECMO run in both modes, and the immunologic balance altered significantly in the VA than in VV mode. Our ECMO model is feasible for the hemodynamic and immunologic research, and further long-term evaluation is needed.