Background Hepatitis B (HB) and Hepatitis C (HC) viral infections, with 328 million cases globally, represent a significant disease burden. Currently, Pakistan has 3.88 million HB and 9.31 million HC cases. High-risk populations like refugees are disproportionately affected by these infections. The objectives of this study were to determine the seroprevalence of hepatitis B surface antigen (HBsAg) and hepatitis C virus antibody (anti-HCV) among Kashmiri refugees in Muzaffarabad, Pakistan, and to identify the key demographic and educational risk factors associated with the seroprevalence in this population. Methods A cross-sectional study was conducted across eight refugee camps in the Muzaffarabad division, Pakistan. A six-membered team visited each camp to collect blood samples through venipuncture. The seroprevalence of HBsAg and anti-HCV was determined using rapid immunochromatographic test (ICT) kits . Results A total of 550 sera samples were collected from the refugee population in Muzaffarabad. The overall seroprevalence was 5.82% (32/550) for HBsAg and 4.73% (26/550) for anti-HCV. A higher seroprevalence of HBsAg and anti-HCV was recorded among females 6.12% (15/245), and 6.53% (16/245), respectively, compared to males 5.75% (17/305), and 3.28% (10/305), respectively. A marked increase in seroprevalence of HBsAg and anti-HCV was noted with an increase in age: 1–10 (2.44%) and (2.44%), 41–50 (8.20%) and (6.56%), and 51–60 (8.93%) and (8.93%), respectively. Chi-square test revealed a statistically significant association between age and seroprevalence of HBsAg χ² (degrees of freedom (df):6, N = 550) = 27.22, p = 0.000, and HC χ² (df:6, N = 550) = 15.23, p = 0.019.The level of education impacted the seroprevalence of HBsAg and anti-HCV, resulting in a higher seroprevalence of HBsAg (6.9%) and anti-HCV (5.4%) among uneducated individuals compared to educated individuals (4.71%) and (3.99%), respectively. Conclusion The seroprevalence of HBsAg and anti-HCV is high among the refugee population of Muzaffarabad, Pakistan. There is a need for the implementation of a robust vaccination program for HB as well as the establishing a hepatitis micro-elimination program among the Kashmiri refugee population of Muzaffarabad, Pakistan.