This study examined the synthesis of magnetic iron oxide nanoparticles coated with PO (FOMNPsP) and assessed their in vitro, ex vivo, and in vivo effects against cystic echinococcosis. The FOMNPsP was synthesized through the alkalization of iron ions in a deoxygenated form. In vitro and ex vivo protoscolicidal effects of FOMNPsP (100–400 μg/mL) were evaluated on hydatid cyst protoscoleces by the eosin exclusion test for 10–60 min. The effect of FOMNPsP on caspase-3 gene expression and exterior ultra-structural of protoscoleces was assessed by real-time PCR and scanning electron microscopy (SEM), respectively. In vivo effects were assessed by evaluating the number, size, and weight of hydatid cysts among infected mice. The FOMNPsP size was < 55 nm, and the most frequent particles were in the 15–20 nm range. In vitro and ex vivo assays revealed that the highest protoscolicidal effect was observed at 400 µg/mL with 100% lethality. After exposure of protoscoleces with FOMNPsP, the level of gene expression of caspase-3 was dose-dependently increased (p < 0.05). By SEM, the FOMNPsP-treated protoscoleces showed wrinkles and bulges resulting from the formation of blebs. FOMNPsP significantly decreased (p < 0.01) the mean number, size, and weight of the hydatid cyst. FOMNPsP revealed the potent protoscolicidal traits through disrupting the cell wall and apoptosis induction. The results also indicated the promising effect of FOMNPsP in controlling hydatid cysts in the animal model. Although FOMNPsP is safe for human normal cells, more investigations are required to clarify its toxicity and precise mechanisms of action.