Cu-modified zeolites provide methane conversion to methanol with high selectivity under mild conditions. The activity of different Cu-sites for methane transformation is still under discussion. Herein, ZSM-5 zeolite has been loaded with Cu²⁺ cations (1.4 wt % Cu) as characterized by UV-vis DRS, EPR, EXAFS, and ¹H MAS NMR. It is inferred that Cu²⁺ cations, attached to the cation-exchange Al−O⁻−Si sites of the zeolite framework, can exist in the form of either isolated or paired Cu²⁺ sites. The transformation of methane to methanol on Cu²⁺/H-ZSM-5 has been verified by the observation of the methoxy species formation with ¹³C MAS NMR and FTIR spectroscopy. The related mechanisms have been analyzed by DFT calculations. The calculations show that the paired Cu²⁺ sites enable heterolytic C−H bond dissociation via the “alkyl” pathway resulting in methylcopper species, which however are not detected experimentally due to further rapid transformation to surface methoxy species through methyl radical formation and recombination with Si−O⁻Al site. Based on the obtained data, it has been concluded that methane transformation to methanol on paired Cu²⁺ sites, having no extra-framework oxygen ligand, is possible in Cu-modified zeolites. The pathways of Cu²⁺ cations regeneration with O₂ and H₂O have been experimentally explored.