Background: Using a 1-year prospective design, we examined the association of organizational justice (i.e., procedural justice and interactional justice) with refraining from seeking medical care (RSMC) among Japanese employees. Methods: We surveyed 2695 employees (1994 men and 701 women) from two factories of a manufacturing company in Japan. A self-administered questionnaire comprising scales for measuring organizational justice (Organizational Justice Questionnaire) and potential confounders (i.e., demographic and socioeconomic characteristics as well as health-related behaviors) was administered at baseline (from April to June 2011). At 1-year follow-up (from April to June 2012), a single-item question was used to measure RSMC during the follow-up period. Multiple logistic regression analysis was conducted by gender. Results: After adjusting for potential confounders, low procedural justice and low interactional justice at baseline were found to be significantly associated with higher odds of RSMC during the 1-year follow-up for male employees (odds ratio = 1.33 [95% confidence interval = 1.16–1.52], p < 0.001 and 1.15 [95% confidence interval = 1.02–1.29], p = 0.019, respectively). Similar patterns were observed for female employees (odds ratio = 1.37 [95% confidence interval = 1.08–1.74], p = 0.009 and 1.23 [95% confidence interval = 1.02–1.50], p = 0.035 for low procedural justice and low interactional justice, respectively). Conclusions: The present study provided evidence that the lack of organizational justice is positively associated with RSMC among Japanese employees, independently of demographic and socioeconomic characteristics as well as of health-related behaviors.