We evaluate the master integrals for the two-loop non-planar box-diagrams contributing to the elastic scattering of muons and electrons at next-to-next-to-leading order in QED. We adopt the method of differential equations and the Magnus exponential to determine a canonical set of integrals, finally expressed as a Taylor series around four space-time dimensions, with coefficients written as combination of generalised polylogarithms. The electron is treated as massless, while we retain full dependence on the muon mass. The considered integrals are also relevant for crossing-related processes, such as di-muon production at e+e− colliders, as well as for the QCD corrections to top-pair production at hadron colliders. In particular our results, together with the planar master integrals recently computed, represent the complete set of functions needed for the evaluation of the photonic two-loop virtual next-to-next-to-leading order QED corrections to μe → μe and e+e− → μ+μ−.