Abstract The model-based design methodology is presented for the development of an experimental SEPIC-MPPT controller powered by a photovoltaic module, designed to extract water from a deep well using a DC submersible motor pump. To specify the proposed methodology, a photovoltaic panel was characterized under various conditions of solar radiation and the modeling of its Voltage-Current relationship was carried out. The best tilt angle for the installation was determined to be nine degrees (9°). Similarly, a SEPIC controller was developed from model-based design. The results obtained showed an average adjustment error of less than 4%, on the performance parameters contrasted in the modeled / experimental system. The efficiency achieved by the SEPIC-MPPT controller was 85.26%. It is concluded that the methodology implemented for the design is coherent and valid for the development of SEPIC-MPPT controllers with application in underground water extraction systems, in areas with photovoltaic potential.