The low-lying electronic excited states of thieno[3,4-b]pyrazine have been studied using the multiconfigurational second-order perturbation CASPT2 theory with extended atomic natural orbital basis sets. The CASPT2 results allow for a full interpretation of the electronic absorption and emission spectra and provide valuable information for the rationalization of the experimental data. The nature, position, and intensity of the spectral bands have been analyzed in detail. A preliminary comparative study of the ground-state geometry of thieno[3,4-b]pyrazine has been performed at the coupled cluster single and doubles and density functional theory levels using a variety of correlation-consistent basis sets. Thieno[3,4-b]pyrazine exhibits a polyene-like structure in the ground state due to the bond localization in the pyrazine moiety. An aromatization of the pyrazine unit is predicted for the lowest-energy electronic excited states.