Background Justice has gained much attention in social and human studies and has many consequences on employees and the organizations, especially on health system workers such as nurses who are among the key factors in health care systems. Objectives The purpose of this study was to investigate perception of organizational justice among nurses in educational hospitals of Shiraz University of Medical Sciences (SUMS), and to compare the results of general and specialty hospitals. Materials and Methods In this research, 400 nurses at SUMS hospitals were selected by random sampling method. A 19-item questionnaire was applied to measure distributive, procedural and interactional justice. Data analysis was performed using descriptive statistics, including percentage, frequency, mean, and standard deviation. Also, the t-test and one way ANOVA were used to measure the differences between different hospitals and wards. Results Of 400 nurses, 66% perceived a high level of organizational justice. In this study the mean scores of total perceived organizational justice (P = 0.035), procedural justice (P = 0.031), and interactional justice (P = 0.046) in specialty hospitals were higher than general ones. Furthermore, the mean score of interactional justice was higher than the other components of organizational justice, respectively 3.58 ± 1.02 for general and 3.76 ± 0.86 for specialty hospitals. Significant differences were observed between overall perceived justice (P = 0.013) and its components (P = 0.024, P = 0.013, and P = 0.036) in different wards. Conclusions Most nurses who participated in this study had a high perception of organizational justice. The mean score of organizational justice was higher in specialty hospitals. Health care policy makers and hospital managers should support their employees, especially nurses through fairness in distributions, procedures, and interactions.