The junction open channel flow is encountered in many hydraulic engineering such as irrigation ditches, wastewater treatment facilities and fish passage conveyance structures. The flow behavior at junction becomes very complex because of the interaction between the branch and main channel, that’s cause many complex problems such as local sedimentary, channel scour and sidewall erosion and others. This paper provides detail application of numerical solution (Finite Volume) by FLUENT-2D software in simulation of 90º open channel junction flows. Numerical simulations undertaken in present two dimensional work use Standard k-ε turbulence model. Comparisons have been made between numerical results and measured experimental velocities of Weber et al. (2001), good agreement between the model predictions and experimental measurements have been obtained. The model is then applied to investigate the dimensions of separation zone. The simulation results show that separation zone size increases as the discharge ratio of the upstream main channel to the downstream channel decreases.