In recent years, diagnosis of diseases worldwide has been of much interest to the scientific community. Among these diagnosis methods, fluorescence spectroscopy has shown promise. Naphthoquinone and their halogenated derivatives have fluorescent properties and the presence of such substituents promote changes in the spectroscopic properties of the compounds. These properties can be studied by time dependent density functional theory methods. Relativistic effects such as spin–orbit coupling, the Hamiltonian relativistic and the basis set including relativistic corrections are essential for the accurate calculation of spectroscopic properties. For the selection of which of these factors are important for the halogenated derivatives naphthoquinone (F, Cl, Br and I) were employed in a factorial design of the 33 Type, known as a Box–Benhken design. It was observed that the DKH2 Hamiltonian and the basis set TVZ_DKH were significant for studying spectroscopic properties of these compounds. Using these parameters, the ESIPT process was investigated for halogenated compounds of naphthoquinone. It was observed that compounds containing Cl, Br and I do not have the ESIPT process, while a compound containing F showed the process having energy values, 4.69 eV for absorption energy, −1.58 eV for the proton transfer energy and 1.87 eV for the emission energy. We believe that the current study can assist in understanding the ESIPT behavior of ANQ derivatives and why the relativistic effects affect this process.