One of the physical methods for obtaining magnetite nanoparticles (NPs) is electron beam physical vapor deposition (EB PVD), which requires complex equipment, but allows obtaining a significant amount of pure (ligand-free) NPs. The biomedical application of such NPs is less studied than materials from other synthesis methods. The objective is to study the effect of pure magnetite NPs in the NaCl matrix obtained by EB PVD on hematological indicators, gases, electrolytes and parameters of iron metabolism in the blood of intact animals. The physical characteristics of NPs were studied using high-resolution transmission electron microscopy, scanning transmission electron microscopy, energy-dispersive X-ray spectroscopy mapping, electron energy-loss spectroscopy, selected area electron diffraction and fast Fourier transform. In vivo experiments were conducted on albino male rats, which were injected with solution of magnetite-sodium chloride NPs (1.35 mg Fe/kg). After 3 and 72 h, hematological parameters, blood gases, electrolytes, and serum iron were determined. The synthesized NPs had an average size of 11 nm. They were identified as magnetite, where polycrystals and single crystals were present. The absence of contamination in crystal boundaries, clear orientation and orderliness of atoms in crystals were established. The administration of NPs in the sodium chloride matrix to animals was characterized by a transient increase in the main indicators of red blood accompanied by an increase in the saturation of erythrocytes with hemoglobin and their mean volume after 3 h. It did not worsen blood gases and pH, but decreased blood Na+ content after 72 h. The investigated NPs caused changes in the parameters of serum iron characteristic to iron preparations, which after 3 h were smaller compared to the reference iron drug, and after 72 h—similar to it. More intense rapid effects on hematological parameters at lower serum iron indicate greater activity of the studied pure magnetite NPs obtained by EB PVD syntesis compared to the reference iron preparation.