This research concentrates on the problem associated with rapid filling of type III hydrogen cylinders in hydrogen-powered aerial vehicles. Rapid filling leads to certain temperature rises in the cylinder due to adiabatic compression and it is jeopardizing the structural integrity. Existing research mainly focused on the effects of pressure variation and temperature rises on hydrogen cylinders. However, there is limited research on the effects of temperature rises in Type III hydrogen storage cylinders incorporated with PTFE-coated aluminium liners under various temperature and mass flow rates related to aerial application. Based on the previous research gap, a 2D axisymmetric cylinder model was developed in ANSYS R21 for a 5 L, 35 MPa Type III PTFE-coated aluminium liner wrapped in carbon fiber hydrogen cylinder. A model analysed under the real gas behaviours through the Redlich-Kwong equation with various inlet conditions of temperature (283–323 K), filling pressure (5–35 MPa) and mass flow rate (0.01–0.05 kg/s). The simulation outcome indicates the increase in internal gas temperature from 293 K to 417 K and the optimum temperature region near the inlet due to recirculatory heating. At a maximum temperature of 323 K, the internal temperature rises up to 600.2K toward the thermal stability limits of PTFE. Due to the insulating properties of PTFE, it reduces the temperature distribution from the inner layer to the outer layer of the cylinder and ensures temperature containment. This research work indicates that a minimum inlet temperature of 283K, a medium filling pressure of 20 MPa, and a moderate mass flow rate of 0.03 kg/s in 6 seconds provide an enhanced thermal stability of the cylinder. This research emphasizes the significance of controlling inlet parameters, not just pressure and flow rate but also temperature, to enhance the safe and efficient lightweight hydrogen storage cylinder used in UAV applications.