At present, there are many software tools that have positively proven themselves for carrying out computational analysis within the framework of assessing the safety of nuclear power utilization facilities. The RELAP5 code, which is intended for carrying out improved assessment of safety, is one of such tools. Initially, its use was limited to a numerical analysis of water-heated water-cooled apparatuses. At the same time, owing to extensive capabilities of the code and stable algorithms for solving hydraulic and thermophysical problems, its application field can be made significantly broader. However, the validity of such broadening should be justified both theoretically and by verification against relevant experimental data. The computational modeling results obtained using the RELAP5 code are given. A comparison between the calculated and experimental data on heating a system operating with low heat fluxes is presented. The results obtained from computations using the RELAP5 code are compared with the results of two experiments. In the first experiment, which was carried out at atmospheric pressure, water was heated in an open thermally insulated vessel. Due to evaporation, the water level in the vessel decreased, but water boiling did not occur. As soon as the water level dropped below the thermal element heated part, the element’s wall temperature showed a sharp increase. The classical approach that was applied to modeling using the RELAP5 code showed a significant discrepancy between the experimental and calculated data. After modifying the computational model, a more adequate agreement between the calculated and experimental results was obtained. In the second experiment, the dewatered system was heated at different heater power levels. With increasing the heater power in successive steps, its temperature changed accordingly. Based on the results from comparison of the calculated and experimental data, it has been shown that the axial heat conduction mechanism has a significant effect on the heating of a partially dewatered heating element, and a method for modeling the longitudinal heat flow along the thermal element in the computations carried out using the RELAP5 code is proposed. The possibility of using the RELAP5 code for simulating a dewatered system has been demonstrated. The verification materials presented in the article contain recommendations for constructing the analysis models of systems operating with low heat fluxes, e.g., spent fuel pools at nuclear power plants.