Core annular flow (CAF) has been proved to be one of the solutions of the heavy oil transportation through pipeline. This study conducted a 3D computational fluid dynamics to simulate CAF of the Newtonian/non-Newtonian Carreau fluid in T- and Y-pipe junctions. The non-Newtonian Carreau fluid was heavy oil (viscosity of 170.811 Pa s at zero shear rate condition) surrounded by water as the Newtonian fluid. The effect of geometry on the flow performance was assessed using the method of 2 k factorial statistical experimental design. For the simulated geometries, the proper design was measured by the high value of oil holdup with small average values of pressure gradient and pressure standard deviation. This condition was predicted to be occurred when adjusting the geometry to the high value of junction angle and pipe diameter. The simulation result showed the stable CAF along the upstream region but then broke up when passing the intersection. © 2022, The Author(s), under exclusive licence to Shiraz University.