An alternative but beneficial way of achieving nitrification and denitrification in activated sludge systems is to apply consecutive aeration and non-aeration periods in a single reactor. In this paper, dynamic modeling and start-up simulation in order to establish the continuous operation mode in such systems are first presented. Newly developed ASM3 is applied to the modeling of microbiological processes in the aeration tank and a 10 layer settling model is adapted to the settling tank. Then, the constrained optimization problem is tackled by an evolutionary algorithm, and the optimum aeration schedule for minimum energy consumption is identified. The constraint handling is achieved by three comparative methods using rejection of infeasibles, penalizing infeasibles and tournament selection without using any penalty parameters. The results indicate that the suggested optimum operation strategy may be economically beneficial in all methods but the third one, which is proposed by Deb [Deb, K. (2000). An efficient constraint handling method for generic algorithms. Computer Methods in Applied Mechanics and Engineering, 186, 311–338] gives better solutions.