The 5-MWth Jordanian research reactor is an open-pool type research reactor using plate-type fuel. It is cooled by the upward natural flow at low power-operation. Natural circulation cooling is important in the safety analysis because it is the last scenario of all accidents. Therefore, studying natural circulation is important in determining the safety limits, such as the maximum allowed temperature and the minimum critical heat flux ratio of fuel. In this paper, the reactor operated at 50KW by the natural circulation to investigate its neutronics and thermal–hydraulic characteristics. Then, the results were benchmarked with RELAP5 MOD 3.3 by implementing models with and without considering the effect of heat loss through the Upper Guide Structure. As a result of this study, different models show minor differences in thermodynamic parameters and an additional safety margin. Eventually, benchmarking the results and the calculations of RELAP5 led to a reasonable agreement in both simulated models.