We present, for the first time, the quantization process for the Einstein-aether scalar field cosmology. We consider a cosmological theory proposed as a Lorentz violating inflationary model, where the aether and scalar fields interact through the assumption that the aether action constants are ultra-local functions of the scalar field. For this specific theory there is a valid minisuperspace description which we use to quantize. For a particular relation between the two free functions entering the reduced Lagrangian the solution to the Wheeler-DeWitt equation as also the generic classical solution are presented for any given arbitrary potential function.