Hemodialysis (HD) patients have an increased risk of severe SARS-CoV-2 infection. In this study, we assess the impact of a third vaccine dose (3D) on antibody levels and T cell response in HD patients and a healthy control group in a prospective cohort study consisting of 60 HD patients and 65 healthy controls. Each participant received two doses of the BNT-162b2 mRNA vaccine and an mRNA vaccine 3D. The SARS-CoV-2 antibody response was measured 6 months after the second vaccine dose and 6 to 8 weeks after the 3D. We assessed INF-γ secretion 6–8 weeks post 3D in 24 healthy controls, 17 HD patients with a normal response, and 20 low responder HD patients. The groups were compared using univariate quantile regressions and multiple analyses. After the 3D, the SARS-CoV-2-specific antibody and INF-γ titers of most HD patients were comparable to those of healthy controls. A subgroup of HD patients who had shown a diminished antibody response after the first two vaccine doses developed a significantly lower antibody and INF-γ response compared to responder HD patients and controls even after the 3D. A new strategy is needed to protect low/non-responder HD patients from severe SARS-CoV-2 infection.