The Universe is homogeneous and isotropic on large scales, so on those scales it is usually modelled as a Friedmann-Lemaítre-Robertson-Walker (FLRW) space-time. The non-linearity of the Einstein field equations raises concern over averaging over small-scale deviations form homogeneity and isotropy, with possible implications on the applicability of the FLRW metric to the Universe, even on large scales. Here I present a technique, based on the multiple-scales method of singular perturbation theory, to handle the small-scale inhomogeneities consistently. I obtain a leading order effective Einstein equation for the large-scale space-time metric, which contains a back-reaction term. The derivation relies on a series of consistency conditions, that ensure that the growth of deviations from the large-scale space-time metric do not grow unboundedly; criteria for their satisfiability are discussed, and it is shown that they are indeed satisfied if matter is non-relativistic on small scales. The analysis is performed in harmonic gauge, and conversion to other gauges is discussed. I estimate the magnitude of the back-reaction term relative to the critical density of the Universe in the example of an NFW halo, and find it to be of the order of a few percent. In this example, the back-reaction term is interpreted as a contribution of the energy-density of gravitational potential energy, averaged over the small-scale, to the total energy-momentum tensor.