The aim of the study was to evaluate the effect of high-flux (HF) hemodialysis (HD) on delayed protective hepatitis B virus (HBV) antibody seroconversion in HD patients who had no response to the classic third dose of HBV vaccination. We performed a prospective cohort study. Forty-two patients who did not respond within 6 months after the third dose of the vaccination were enrolled in the study. The patients were randomized to either an HF HD treatment group (n =19) or a conventional HD treatment group (n = 23). Patients' serum hepatitis B surface antibody levels were followed monthly. After 6 months of follow-up, there were 15 (78.9%) patients in HF group and 7 (30.4%) patients in the control group showing delayed HBV vaccination response. The level of antibody titer of HBV vaccination responders was 103.6 ± 48.3 mIU/mL in the HF group and 23.5 ± 15.7 mIU/mL in the control group. The antibody titer did not correlate with sex, age, serum albumin, or hemoglobin in either group. Four patients in control group lost HBV vaccination response > 2 times after 3 months of follow-up, whereas no patients in the HF group lost HBV vaccination response. Hemodialysis patients who do not respond to the classic third dose of HBV vaccination could reobtain a delayed higher protective HBV antibody seroconversion rate by HF HD without other intervention.