Background: Influenza vaccine uptake among healthcare workers is crucial for preventing influenza infections, yet its effectiveness needs further investigation. Objectives: This prospective observational study aimed to assess the protective effect of influenza vaccination among healthcare workers in Shenzhen. Methods: We enrolled 100 participants, with 50 receiving the 2023–2024 quadrivalent influenza vaccine (QIV) and 50 serving as unvaccinated controls. Epidemiological data were collected when the participants presented influenza-like illness. Serum samples were collected at three time points (pre-vaccination and 28 and 180 days after vaccination). Hemagglutination inhibition (HI) assay was performed against the strains included in the 2023–2024 QIV (H1N1, H3N2, BV and BY strains) to assess antibody protection levels. Demographics comparisons revealed no significant differences between the vaccinated and control groups (p > 0.05), ensuring group comparability. Results: The incidence of influenza-like illness was significantly lower in the vaccinated (18%) compared to the control group (36%; p = 0.046; OR = 0.39; 95% CI: 0.15 to 0.98). The vaccinated group also exhibited a higher rate of consecutive two-year vaccinations (48% vs. 24% in the control group, p < 0.05). Additionally, the vaccinated healthcare workers were more inclined to recommend vaccination to their families (80% vs. 48%, p < 0.05). HI titers against H1N1 (p < 0.01), H3N2 (p < 0.01), BV (p < 0.001) and BY (p < 0.01) significantly increased in the vaccinated group at 28 days post-vaccination. Moreover, a marked and sustained increase in HI titers against the H3N2 strain (p < 0.001) was observed at 180 days post-vaccination, highlighting the vaccine’s enduring impact on the immune response. The fold change in the HI titers, indicative of the magnitude of the immune response, was significantly higher for H1N1 (p < 0.01), H3N2 (p < 0.001), BV (p < 0.01) and BY (p < 0.05) among the vaccinated individuals compared to the control group, underscoring the vaccine’s efficacy in eliciting a robust and sustained antibody response. Conclusion: Influenza vaccination significantly reduces the incidence of influenza-like illness among healthcare workers and promotes a sustained immune response. The study supports the importance of annual vaccination for this group to enhance personal and public health.