To compare surrogate markers of immunogenicity between recombinant and inactivated influenza vaccines, this study conducted a systematic review and meta-analysis for each strain. Three databases of Medline (Pubmed), Embase and Cochrane Central were searched to identify all published literature up to July 2023. Out of a total of 1,658 initially identified articles, 14 randomized controlled trials were selected based on inclusion and exclusion criteria. The program R version 4.3.1 was used to estimate the mean difference of geometric mean titer (GMT) and the pooled risk ratio (RR) of seroconversion and seroprotection with 95% confidence intervals. The meta-analysis results found higher GMT effect sizes for recombinant influenza vaccines compared to inactivated vaccines for A/H3N2 (MD=124.87, 95% CI 52.63-197.11) and B/Yamagata (MD=19.89, 95% CI 7.61-32.17) strains. In terms of seroconversion rates, recombinant influenza vaccines exhibited higher seroconversion for A/H3N2 (RR=1.33, 95% CI 1.26-1.40) and B/Yamagata (RR=1.75, 95% CI 1.06-2.89) strains. Slightly higher seroprotection rates were observed for A/H3N2 (RR=1.04, 95% CI 1.02-1.07) and B/Yamagata (RR=1.07, 95% CI 1.01-1.13) strains with recombinant vaccines. The findings from this study contribute valuable evidence for regulatory decisions when introducing recombinant vaccines in South Korea.