We address the issue of radiative corrections to Kaluza-Klein (KK) masses in five-dimensional QED supplemented by aether Lorentz-violating terms. Specifically, we compute the corrections to the KK photon masses from one fermion loop. In general, the KK masses receive radiative corrections due to breaking the five-dimensional Lorentz invariance by compactification. As we show, the presence of the additional Lorentz violating factor - an aether background, leads to the non-trivial modification of these corrections. This model may be of interest in addressing important phenomenological issues such as the relation between radiative corrected KK mass splitting of a particular mode and uncertainties in the measurements and/or possible spatial variation of the fine-structure constant. For the recent data on the fine-structure constant, we find a KK mass splitting of magnitude $sim 0.01$ MeV for the first excited Kaluza-Klein gauge boson at TeV scale. On the other hand, the large KK modes limit displays a very interesting phenomenon, showing the very special role of the aether in protecting the higher modes from the quantum corrections.