This paper presents a fuzzy logic controller (FLC) based on output reference tracking operation applied to a photovoltaic system (PV) with a single-ended-primary-inductor converter (SEPIC). The SEPIC DC/DC converter has multiple applications as a power conditioning system because it has a non-pulsating input current and its voltage ratio is both step-down and step-up. Comparisons between simulations and experimental results about input requirements, output ripple voltage and efficiency are presented. The performance of the converter is tested in both simulation and experiment at different operating conditions. Finally, the results show that the proposed FLC based output reference tracking strategy can accurately track the reference signal applied to photovoltaic systems.