The evolution of parasite resistance to antiparasitic agents has become a serious health issue indicating a critical and pressing need to develop new therapeutics that can conquer drug resistance. Nanoparticles are novel, promising emerging drug carriers that have demonstrated efficiency in treating many parasitic diseases. Lately, attention has been drawn to a broad-spectrum nanoparticle capable of converting absorbed light into heat via the photothermal effect phenomenon. The present study is the first to assess the effect of silver nanoparticles (Ag NPs) and iron oxide nanoparticles (FeO NPs) as sole agents and with the combined action of the light-emitting diode (LED) on Blastocystis hominins (B. hominis) in vitro. Initially, the aqueous synthesized nanoparticles were characterized by UV-Vis spectroscopy, zeta potential, and transmission electron microscopy (TEM). The anti-blastocyst efficiency of these NPs was tested separately in dark conditions. As these NPs have a wide absorption spectrum in the visible regions, they were also excited by a continuous wave LED of wavelength band (400-700 nm) to test the photothermal effect. The sensitivity of B. hominis cysts was evaluated using scanning laser confocal microscopy whereas the live and dead cells were accurately segmented based on superpixels and the k-mean clustering algorithm. Our findings showed that this excitation led to hyperthermia that induced a significant reduction in the number of cysts treated with photothermally active NPs. The results of this study elucidate the potential role of photothermally active NPs as an effective anti-blastocystis agent. By using this approach, new therapeutic antiparasitic agents can be developed.