State-of-the-art computational tools were used to investigate the photophysical properties of polyfluorinated phthalocyanines (Pc) to predict their potential use as photo sensitizers in photodynamic therapy. The main factors, such as the identity of the metal ion, the effect of substituents, the environment, and solvent effects that enhance the efficiency of phthalocyanines as photosensitizers, were considered, particularly taking into account their influence on the triplet-state energy and intersystem crossing probability. The population of the triplet state ultimately determines the phthalocyanine's propensity to activate singlet oxygen, which is responsible for inducing death of the cancer cell. Time-dependent density functional theory was used to elucidate the photophysical properties of pentafluorobenzyloxy-substituted phthalocyanines (R2Pc) as well as their unsubstituted analogues. Vibrational and dynamic effects influencing the absorption and emission spectra were included by sampling the potential energy surfaces via the Wigner distribution approach. Furthermore, the intersystem crossing pathways were analyzed by using the singlet-triplet band gap and the spin-orbit coupling constant. Finally, the singlet oxygen generation capability was experimentally verified for the R-2-ZnPc complex both in DMSO and in different ratios of DMSO/water mixtures. The singlet oxygen quantum yield of R-2-ZnPc in DMSO was also evaluated and compared with that of the unsubstituted ZnPc.