Refuelling hydrogen-powered cars, buses, trucks, trains, ships, and planes is a technological challenge. The absence of contemporary CFD models of refuelling through the entire hydrogen refuelling station (HRS) equipment is one of the scientific bottlenecks. Detailed refuelling protocols for more than 10 kg of hydrogen, e.g., for heavy-duty vehicles, are absent. A thoroughly validated CFD model for simulations of the refuelling process through the entire equipment of the HRS is needed for protocols’ development. This study aims to numerically simulate the start-up phase of the refuelling procedure at HRS using the developed CFD model. The simulations through the entire HRS equipment are compared against unique experimental data of NREL and demonstrated agreement with measured pressure and temperature dynamics in onboard storage tanks during the start-up phase while having less than 5% deviation. The CFD model demonstrates excellent predictive capability and is time efficient. The simulation time of the start-up phase of 14 s duration is about 2 h on a 32-core CPU.