Irrigation is one of the sectors in which energy consumption is increasing, mainly due to modernized systems designed to conserve water through the use of pressurized water distribution. Energy is one of the principle costs in irrigation. In this study, a new methodology is developed to determine the minimum total water application cost (investment+operation costs) in center pivot systems withdrawing water from wells. The proposed methodology optimizes the characteristic and efficiency curves for the pump as well as the types and diameters of pipes for pumping and distribution. In addition, the method accounts for hydrological variables (dynamic water table level and temporal variation), soil variables (infiltration parameters, surface storage capacity, surface impermeability), hydraulic variables (head losses in pipes, flow demand) and economic variables (energy costs, pump and pipe costs). In order to facilitate the technology transfer to managers and technicians, free software (DOP, “Diseño Optimo de Pivotes,” or Optimal Pivot Design) has been developed using MATLAB™. Results show that the best options are timing irrigation to avoid periods of high energy costs as well as increasing pumping power and pipe size, with a greater system capacity (1.5Ls−1ha−1), and shorter operation time (18hday−1). The minimum water application cost is obtained in all case studies in this paper for center pivot systems irrigating 75ha, with lateral pipes of 254mm (10in.).