Central venous catheter (CVC) related thrombosis is a major cause of CVC dysfunction in patients under hemodialysis. The aim of our study was to investigate the impact of CVC insertion on hemodynamics in the central veins and to examine the changes in hemodynamic environments that may be related to thrombus formation due to the implantation of CVC. Patient-specific models of the central veins with and without CVC were reconstructed based on computed tomography images. Flow patterns in the veins were numerically simulated to obtain hemodynamic parameters such as time-averaged wall shear stress (TAWSS), oscillating shear index (OSI), relative residence time (RRT), and normalized transverse wall shear stress (transWSS) under pulsatile flow. The non-Newtonian effects of blood flow were also analyzed using the Casson model. The insertion of CVC caused significant changes in the hemodynamic environment in the central veins. A greater disturbance and increase of velocity were observed in the central veins after the insertion of CVC. As a result, TAWSS and transWSS were markedly increased, but most parts of OSI and RRT decreased. Newtonian assumption of blood flow would overestimate the increase in TAWSS after CVC insertion. High wall shear stress (WSS) and flow disturbance, especially the multidirectionality of the flow, induced by the CVC may be a key factor in initiating thrombosis after CVC insertion. Accordingly, approaches to decrease the flow disturbance during CVC insertion may help restrain the occurrence of thrombosis. More case studies with pre-operative and postoperative modeling and clinical follow-up need to be performed to verify these findings. Non-Newtonian blood flow assumption is recommended in computational fluid dynamics (CFD) simulations of veins with CVCs.