A systematic approach to determine the optimal operation strategy for nitrogen (N) and phosphorus (P) removal of sequencing batch reactors (SBRs) has been developed and applied successfully to a lab-scale SBR. The methodology developed is based on using a grid of possible scenarios to simulate the effect of the key degrees of freedom in the SBR system. The grid of scenarios is simulated using a calibrated ASM2dN model developed and calibrated in a previous study. Effluent quality in combination with a robustness index for each of the scenarios is used to select the best scenario. With the best scenario, it is possible to improve/increase the current performance of the SBR system by around 54% and 74% for N and P removal respectively.