Aim <p>In response to the increasing experiences of loneliness and declining well-being among university students, the aims of this research were to determine the characteristics of students who perceive university injustice, and to investigate the associations among perceived university injustice, loneliness, and well-being among German university students.</p> Subject and methods <p>We assessed perceived university injustice (University Fairness Questionnaire; UFair), loneliness (6-item De-Jong-Gierveld Scale), well-being (WHO-5 Well-being Index), and sociodemographic, socioeconomic, and study-related determinants in a nationwide survey of 1,105 university students. In addition to bivariate statistics, regression models, and a mediation analysis (the PROCESS macro by Hayes) were used to identify associations between perceived university injustice, loneliness, and well-being.</p> Results <p>The findings indicate higher levels of perceived university injustice among international students (3.14 vs. 2.47, p &lt; 0.001), male students (2.77 vs. 2.39, p &lt; 0.001), students receiving funding from the Federal Law on Support for Education (2.78 vs. 2.50, p &lt; 0.001), and students with side jobs (2.63 vs. 2.49, p = 0.013). In addition, perceived university injustice was associated with general (β = 0.327, p &lt; 0.001), emotional (β = 0.334, p &lt; 0.001), and social loneliness (β = 0.205, p &lt; 0.001). The mediation analysis revealed that perceived university injustice had an indirect negative effect on the well-being of students (β = -0.114, p &lt; 0.05) through the mediating factors of emotional and social loneliness.</p> Conclusion <p>This study emphasizes the need for greater awareness of perceived university injustice in higher education to create a supportive environment, in which students feel cared for and are both socially and emotionally connected in order to improve students’ well-being in academic settings.</p>