Fish cellular models are commonly used to study the toxic potential of environmentally relevant compounds. Several of these pollutants act on DNA and compromise its integrity. Little is known, however, about the DNA repair ability of these cellular models. Therefore, the aim of this study was to evaluate the DNA base excision repair (BER) of zebrafish Liver (ZF-L) cell line and primary hepatocytes. We performed kinetic studies of the DNA damage levels after exposure to hydrogen peroxide (HO, 20 μM for 10 min) using the Comet Assay. Ten minutes after HO treatment, 16% and 50% of the initial damage, measured as comet tail length, were repaired in ZF-L cell line and primary hepatocytes, respectively. Primary hepatocytes repaired 50% of the damages twice as fast as ZF-L cell line and showed DNA damage levels similar to control 40 min after HO treatment. The total recovery time for ZF-L model was of 180 min, which indicates the culture cells have a less efficient BER. In conclusion, both ZF-L cell line and primary hepatocytes exhibit BER activity; however, these cellular models have different repair capacity. In addition, we demonstrated that ZF-L cell line and primary hepatocytes are useful tools for ecotoxicological studies focusing on DNA single-strand breaks and BER.