In Indian population, hepatitis C virus (HCV) genotypes 1 and 3 are prevalent and predominant with the highest frequency. However, other genotypes are seldom reported, and among them the HCV genotype 5a is exceptionally rare. The presented case had no history for either blood transfusion or using any type of IV drugs and never traveled to any other country. He was serologically positive with HCV antibodies and HCV RNA. 5'UTR-specific amplification and sequencing of infected viral genome confirmed that he had been infected with HCV genotype 5a which is not closely related to other common prevalent genotypes like 1a, 1b, 3a, and 3b in India. Patient's wife and children tested negative for anti-HCV and HCV-RNA. This unique case report could be attributed to circulation of HCV genotype 5a from other geographic area at very low frequency in India as determined by phylogenetic analysis and nucleic acid-sequencing methods.