Hepatitis C virus (HCV) core protein can form capsid-like particles and is believed to be the viral capsid protein. Besides its structural functions, this protein is also known to possess multiple regulatory functions. In this article, we have studied the possible phosphorylation of HCV core protein in two different human liver-derived cell lines Huh7 and HepG2. Our results indicated that the HCV core protein could be phosphorylated, albeit inefficiently, independent of its downstream E1 protein in these two cell lines. Two of the basal phosphorylation sites were identified to be serine-53 and serine-116. The phosphorylation of the core protein could be enhanced by the PKC activator phorbol 12-myristic 13-acetate (PMA), and the PKA activator forskolin, and these enhancements could be abolished by the respective inhibitors of PKC and PKA, indicating that the core protein is a substrate of these two kinases. While both serine-53 and serine-116 served as the PKC phosphorylation sites, serine-116 appeared to be the major PKA phosphorylation site. Further analyses using serine-to-alanine mutation to mimic dephosphorylation and serine-to-aspartic acid mutation to mimic phosphorylation revealed that the conversion of serine-116 to aspartic acid led to an enhanced nuclear localization of the core protein. This observation indicates that one function of phosphorylation may be to regulate the nuclear localization of the core protein.