As an important step towards a complete next-to-leading order (NLO) QCD analysis of the ratio $varepsilon/varepsilon$ within the Standard Model Effective Field Theory (SMEFT), we present for the first time the NLO master formula for the BSM part of this ratio expressed in terms of the Wilson coefficients of all contributing operators evaluated at the electroweak scale. To this end we use the common Weak Effective Theory (WET) basis (the so-called JMS basis) for which tree-level and one-loop matching to the SMEFT are already known. The relevant hadronic matrix elements of BSM operators at the electroweak scale are taken from Dual QCD approach and the SM ones from lattice QCD. It includes the renormalization group evolution and quark-flavour threshold effects at NLO in QCD from hadronic scales, at which these matrix elements have been calculated, to the electroweak scale.