Sequencing Batch Reactors have become a widely used technology for reject water treatment. SBR is a fill-and-draw system where the biological processes are identical to the conventional activated sludge process. Knardalstrand wastewater treatment plant in Porsgrunn recently upgraded the plant with two full-scale SBRs with working volumes of 115 m³ and 100.4 m³. The objective of this project was to model and simulate the biological process in SBR using GPS-X. GPS-X is a wastewater modelling and simulation software designed for optimizing upgraded municipal wastewater treatment plants. Two SBR models in GPS-X were developed for ammonia nitrogen (NH₄-N) removal in a simple and advanced model environment. The model simulation result has shown that the advanced SBR model was robust and predicted well the process in the real plant than the simple SBR model. The advanced SBR model’s ammonia removal efficiency through nitrification increased with an increase in dissolved oxygen (DO) concentration. However, the nitrogen mass balance analysis showed that the advanced SBR model had higher nitrogen removal efficiency of 75% at a DO setpoint of 1.5 mg/L through shortcut partial nitrification-denitrification. In all the simulations there was high nitrite (NO₂^-) accumulation in the reactors, which could be due to the partial nitrification coupled with denitrification. The simulation has showed the presence of simultaneous nitrification-denitrification process in the full-scale SBR plant. We conclude that the accuracy of the advanced SBR model can be improved by quality input data and accurate representation of physical characteristics in the advanced model environment. Moreover, optimization of the simultaneous nitrification and denitrification in the full-scale SBR has a huge potential to reduce the operational energy cost through reduction of DO setpoints.