Background/Objectives: Low blood vitamin D levels have been linked to COVID-19 severity; however, data on the effects of vitamin D on vaccine immunogenicity remain limited. This study evaluated the impact of baseline serum 1α, 25-(OH)2 vitamin D, a bioactive form with controlled blood concentrations, on vaccine response. Methods: From June to September 2021, we measured active vitamin D levels in 88 Japanese workers and students before vaccination with BNT162b2 or mRNA-1273. We assessed SARS-CoV-2 spike protein S1 IgG and IgM levels and antigen-specific INF-γ-releasing cells from pre-vaccination up to 8 months post-second dose. Results: Active vitamin D levels ranged from 33.7 to 99.8 pg/mL, 60.2% above the Japanese reference range (20–60 pg/mL). In a mixed model accounting for repeated measures and sub-cohort random effects and following fixed effects, vaccine type, weeks post-vaccination, age, sex, ALDH2 gene polymorphism, height, smoking, ethanol intake, exercise, stress, steroid use, allergies, dyslipidemia, active vitamin D was negatively associated with anti-S1 IgG and IgM (p < 0.001) but positively with INF-γ-releasing cell counts (p = 0.003). Conclusions: As the robustness of cellular immunity is independent of viral mutations, 1,25-(OH)2 vitamin D levels above the reference range may enhance vaccine-induced COVID-19 protection in the long term.