(1) Background: Shift work can affect physical health and the immune system by altering the body's circadian rhythms. This study investigated the factors associated with the hepatitis B virus (HBV) vaccination response in manufacturing workers, classified by whether they engaged in shift work or not. (2) Methods: This retrospective observational study was conducted among adults employed at two manufacturing companies. Those with negative initial hepatitis B surface antibody (HBsAb) levels before vaccination and who subsequently received a three-dose series of HBV vaccine were enrolled. Hepatitis B surface antibodies were examined for 3 years after the first dose. The endpoint of this study was the failure of a seroprotective anti-HB response after vaccination (HBsAb < 10 mIU/mL). Binary logistic regression models were used to analyze factors associated with response failures. (3) Results: Of the 1103 eligible subjects, 337 (30.6%) were shift workers. The failure rate was numerically higher in the shift workers (9.2%) than in the non-shift workers (7.9%), without statistical significance (p = 0.405). However, after adjustment with the binary logistic regression models, the shift workers had a statistically significantly higher rate of response failures than the non-shift workers (odds ratio 2.87; 95% confidence interval 1.64-5.05, p < 0.001), as did males, older workers, those with a low initial anti-HB titer, those with a vitamin D deficiency, and current smokers. (4) Conclusions: Our findings suggest a possible association between shift work and the serologic responses to HBV vaccination. Novel strategies for vaccination should be considered for shift workers.