Introduction: Hepatitis C virus (HCV) infection is a major public health problem which influences about 170 million people worldwide. Different types of vaccines have been designed using HCV structural proteins to control the viral infection. The core nucleocapsid protein is one of the most conserved proteins and a desirable target for HCV vaccines, especially the protein-based vaccines. In current study, we generated the core protein recombinantly in prokaryotic (Escherichia coli) and eukaryotic (Leishmania tarentolae) expression systems and compared the humoral immune responses stimulated by each protein in a BALB/c mice model. Methods: The expression of HCV core protein was performed using the prokaryotic pET-28a/ BL21 expression system and also the eukaryotic LEXSY expression system. The recombinant core proteins expressed in E. coli and Leishmania were purified using reverse staining method and affinity chromatography under native conditions, respectively. The purified core proteins were detected by SDS-PAGE and Western blotting using anti-His antibody and were assessed by NanoDrop spectrophotometer. Finally, the abilities of both recombinant core proteins to induce the effective humoral immune responses were evaluated using indirect ELISA. Results: Our data indicated a clear band of ~ 21 kDa for the purified HCV core proteins in both expression systems, confirmed by SDS-PAGE and Western blotting. The mice immunization with both recombinant core proteins was able to produce high levels of antibody isotypes (IgG1 and IgG2a) in comparison with the controls (p < 0.05). In addition, the level of IgG2a response was significantly higher in the group immunized with the core protein purified from leishmania compared to the protein generated from E. coli (p < 0.05). Conclusion: The recombinant core protein generated by the leishmania expression system could induce a Th1-biased immune response with respect to the increase of IgG2a to IgG1 ratio.