An iron oxide nanosystem (Fe3O4Nps) encapsulated with chitosan under the adsorption of hexadecafluorozinc phthalocyanine (ZnPcP16) was developed. The synthesis of Fe3O4Nps was carried out through coprecipitation, followed by coating the nanoparticles with chitosan and incorporation with ZnPcP16. To understand and describe the mechanism of action of Fe3O4Nps-Chitosan-ZnPcP16, we use a variety of physicochemical characterization approaches. Electron microscopy results confirmed the monodispersity of the nanoparticles (13.2 ± 2.3 nm). Size distribution and surface charge (zeta potential) were determined by a dynamic light scattering (DLS) analyzer. VSM measurements confirmed its magnetic properties (1.18 emu.g−1). XDR confirmed the crystalline nature of the nanoparticles. UV-visible absorption and fluorescence spectra were used to evaluate the photophysical behavior of ZnPcP16 and Fe3O4Nps-Chitosan-ZnPcP16. These studies have demonstrated good results through synthesizing Fe3O4Nps-Chitosan-ZnPcP16, which could be a promising candidate for applications in photodynamic therapy.