Assessment of different ab initio and TDDFT methods was studied for calculation of the excitation energies of the complexes of pyrimidine bases with positively charged Ag₃⁺clusters. Performance of CIS, CIS(D), CC2, ADC(2), MP2, and TDDFT techniques with the use of different hybrid–GGA and meta–hybrid–GGA functionals and basis sets is studied. We found that M06–2X functional shows good accuracy in comparison with the ADC(2) ab initio method and that the geometry optimization approach can strongly affect the excitation spectra of the complexes. Our results may have important implications for further studies of ligand–stabilized silver nanoclusters.