We present a calculation of the NLO QCD corrections to Higgs boson pair production within the framework of a non-linearly realised Effective Field Theory in the Higgs sector, described by the electroweak chiral Lagrangian. We analyse how the NLO corrections affect distributions in the Higgs boson pair invariant mass and the transverse momentum of one of the Higgs bosons. We find that these corrections lead to significant and non-homogeneous K-factors in certain regions of the parameter space. We also provide an analytical parametrisation for the total cross-section and the m(hh) distribution as a function of the anomalous Higgs couplings that includes NLO corrections. Such a parametrisation can be useful for phenomenological studies.