Abstract This work investigates the impact of acoustically treated intakes on fan flutter. The propagation of the fan acoustic perturbations is studied using a simplified model, where the frequency of the waves in the intake is the natural frequency of the fan blade in the stationary frame of reference. The model consists of a constant cross-section annular duct, where the acoustic modes are computed for hard wall and lined wall regions, assuming a uniform axial flow. The interfaces between the lined and hard wall sections are solved by doing mode matching. The acoustic reflections in the zero-thickness intake are computed using the Wiener-Hopf technique following Rienstra's model. Analytical results show that the waves propagating from the fan are reflected and scattered radially at the interfaces between the hard wall and the liner. Furthermore, the liner damps and changes the phase velocity of acoustic modes. Due to the low frequency of the flutter waves, the radial scattering can activate different cut-off modes, which need to be retained in order to make accurate predictions. The likelihood of fan flutter is estimated using the phase of the reflected cut-on waves reaching the fan. This strategy is used to assess the impact of the acoustic liners on the stability of a realistic fan. It is concluded that the impact of the phasing and reflections induced by the acoustic liners is comparable to that of the intake and can alter the flutter characteristics of the fan significantly.