Facing rapid changes and fierce competition in the fourth industrial revolution era, organizations have actively employed job rotation as one of the human resource management strategies. Job rotation can play a crucial role in improving individual and organizational competitiveness, and employees’ perception of job rotation can significantly influence individual and organizational outcomes. This study focuses on the perception of organizational justice in job rotation based on organization justice theory and aims to explore its effect on employees’ job satisfaction and organizational effectiveness. In addition, considering that the organization is a heterogeneous group of various age cohorts, we also investigate how different age cohorts affect this process. To test the hypotheses, we conducted an empirical study on 250 employees consisting of Generation X and Millennials working in domestic (South Korean) organizations. The results showed that, among the three dimensions of organizational justice, distributive justice is positively related to job satisfaction, which in turn leads to organizational effectiveness (i.e., organizational commitment, job performance, and turnover intention). In addition, the relationship between interactional justice in job rotation and job satisfaction is stronger in Generation X than in Millennials, while the one between job satisfaction and job performance is stronger in Millennials than in Generation X. Based on the findings of this study, we provide important theoretical and practical implications on how the perception of organizational justice in job rotation influences employees’ job satisfaction and organizational effectiveness, and how differences in generation affect this influencing mechanism.