In this study, the greenreverse-phase liquid chromatography (RPLC) method was used in addition to the traditional RPLC method to determine the ionization/protonation constants (pKa) of the guanine derivatives ganciclovir, valacyclovir, and valganciclovir. The determination of these values was carried out in binary acetonitrile–water mixtures (for the traditional RPLC method), ethanol–water binary mixtures (for the green RPLC method), and in aqueous solution of a micelle-forming surfactant (for pure micellar chromatography). The pKa values sspKa of the compounds were calculated using the linear solvation energy relationship (LSER) method in the studied hydro-organic and micellar solvent-free mixtures. Moreover, the UV–Vis spectrophotometric method was used to compare the sspKa values of ganciclovir, valaciclovir, and valganciclovir obtained in a acetonitrile–water medium using another method. The pKa values of the examined compounds in water were calculated using the linear relationship between the sspKa values determined in hydroorganic mixtures and some macroscopic values of acetonitrile and ethanol. Additionally, wwpKa values were determined in the micellar solvent-free mobile phase. Subsequently, the wwpKa values calculated by these direct and indirect methods were compared and the agreement between them was excellent. By using the wwpKa value calculated for each compound, the ionization percentages were calculated at different pH (1–12) values with the Henderson-Hasselbalch equation. The environmental impact of the RPLC methods used in this study was assessed using the green metrics tools GAPI and AGREE. The result of the investigation was that the environmental suitability of the green methods is satisfactory.