Hepatitis C virus (HCV) infection is one of the major global health problems, particularly for people who inject drugs (PWID). This study aimed to investigate the spontaneous clearance rate of HCV and associated factors with the clearance among PWID using an HCV core antigen (HCV-cAg) test. Blood samples were collected from 311 male PWID concentrated in a rehabilitation center in Haiphong,Vietnam, every 6 months for up to 18 months from 2007, and analyzed serologically and genetically. Of the 311, 240 (77.2%) were positive for anti-HCV antibody (HCV-Ab), and 219 (70.4%) for HCV-cAg,though three HCV-cAg positives were negative for HCV-Ab. Of the 219, 52.5% were co-infected with human immunodeficiency virus (HIV). The most prevalent HCV genotype was genotype 1 (45.7%),followed by genotypes 6 (40.6%), and 3 (7.6%). Spontaneous clearance of HCV-cAg was observed in 12 (5.5%) of 219 PWID during the observation period, and the clearance rate was 6.5 per 100 personyears (95% confidence interval, 3.5–11.3). HCV-cAg level was marginally higher in PWID co-infected with HIV than those without HIV (p = 0.054) and lower in PWID with HCV genotype 3 than those with other genotypes (p < 0.001). Only low HCV-cAg level at baseline was associated with HCV clearance (p < 0.001). HCV-cAg level correlated with the HCV-RNA load in plasma at baseline (Rho = 0.55, p <0.001). Low HCV-cAg level at baseline could be a predictor of HCV clearance. HCV-cAg test could be applicable for HCV screening and used for monitoring plasma HCV load.