Perception of (in)justice has reached significant scientific interest in divers areas of social sciences; especially in the field of organizational psychology. However, it has not been widely studied in the academic environment. Therefore, the aim of this research was to provide a better understanding of justice perception in institutional context by examining its connection to work engagement and counterproductive organizational behavior, and by viewing emotions as potential mediators of those relationships. In total 426 students of the University of Zagreb filled in an online questionnaire which included Teachers’ and Peers’ Fairness Scale, Affective Well-Being Scale for Students, Work Engagement Scale, and Counterproductive Work Behavior Questionnaire for Student Population. Data analysis revealed a significant and positive relationship between four dimensions of justice perception and work engagement and indicated that measures of counterproductive work behavior have a different pattern of connections with justice perceptions. Namely, only interactional justice of colleagues was significantly and negatively connected to interpersonal deviance, while procedural and interpersonal fairness of teachers were significantly and negatively related to organizational deviance. Also, positive emotions explained the significant variance of work engagement above the dimension of justice and mediated their relationships with work engagement. Contrary to the expected, positive and negative emotions did not show unique contribution in predicting dimension of counterproductive work behavior above fairness. Presented results confirmed the relevance of justice perceptions in the academic environment and provided guidelines for developing the context which could foster pleasant emotions and greater students' engagement.