Background: The hepatitis C virus (HCV) infection is a candidate disease for micro-elimination. Accurate baseline HCV prevalence estimation is essential to monitor progress to micro-elimination but can be methodologically challenging in low-endemic regions like the Netherlands due to lack of disaggregated data by age or risk-groups on the number of chronic HCV patients (i.e. HCV RNA positive). This study estimates the number of patients that has had a chronic HCV infection (ever-chronic) in the Utrecht region of the Netherlands. Methods: In the Utrecht province in the Netherlands, positive HCV tests from the period 2001–2015 from one diagnostic center and four hospital laboratories were collected. A two-source capture-recapture method was used to analyze the overlap between the two registries (with 92% HCV RNA and 8% HCV immunoblot confirmed infections) to obtain the number of ever-chronic HCV infections in the Utrecht region. The Utrecht region was defined as an area with a 25 km radius from the Utrecht city center. The current viremic HCV prevalence was calculated by taking into account the proportion of cured and deceased HCV patients from a local HCV retrieval (REACH) project. Results: The estimated number of ever-chronic HCV patients was 1245 (95% CI 1164–1326) and would indicate a prevalence of 0.10 (95% CI 0.09–0.10) in the Utrecht region. This is 30% (95% CI 21–38%) more than the number of known HCV patients in the records. The ever-chronic HCV prevalence was highest in the 1960–1969 age cohort (0.16; 95% CI 0.14–0.18). Since 50% of the HCV patients were cured or deceased in the REACH-project, the number of current viremic HCV patients was estimated at 623 individuals in the Utrecht region (prevalence 0.05%). Conclusion: The results of this study suggest a low ever-chronic and current HCV prevalence in the Utrecht area in the Netherlands, but other studies need to confirm this.