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Three-dimensional throughflow models represent a turbomachinery cascade via a force distribution without the need for detailed geometric modelling in the numerical solution, saving consistent computational resources. In this paper, we present the application of a body force method on an axial transonic fan implemented into an in-house tool for axisymmetric throughflow simulations. By a systematic comparison of local and integral quantities with a validated numerical solution, the capabilities and limitations of the model are discussed for different operating regimes. The implementation is first validated at the peak efficiency calibration point, providing a good duplication of blade flow variables and radial profiles. The design total pressure is matched with a 0.6% absolute difference and a slightly higher slope of the characteristic towards the stall. The isentropic efficiency curve is penalised after the choking mass flow rate calibration, presenting an absolute difference close to 2%, although with a consistent off-design trend. In general, the model provides a satisfactory representation of the flow field and the outflow spanwise distributions, with locally larger discrepancies near the endwalls. Finally, the method is applied to simulate the fan and outlet guide vanes installed into an isolated turbofan nacelle. The onset of intake stall at a high angle of attack is compared between the body force and a boundary conditions-based approaches, highlighting the importance of adopting fully coupled solution methods to study fan/airframe interaction problems.