The instability of the hub vortex observed in wind turbine wakes has recently been studied by Iungo et al. (J. Fluid Mech., vol. 737, 2013, pp. 499–526) via local stability analysis of the mean velocity field measured through wind tunnel experiments. This analysis was carried out by neglecting the effect of turbulent fluctuations on the development of the coherent perturbations. In the present paper, we perform a stability analysis taking into account the Reynolds stresses modelled by eddy-viscosity models, which are calibrated on the wind tunnel data. This new formulation for the stability analysis leads to the identification of one clear dominant mode associated with the hub vortex instability, which is the one with the largest overall downstream amplification. Moreover, this analysis also predicts accurately the frequency of the hub vortex instability observed experimentally. The proposed formulation is of general interest for the stability analysis of swirling turbulent flows.