Magnetic Fe₃O₄ nanoparticles (NPs) and their surface modification with therapeutic substances are of great interest, especially drug delivery for cancer therapy, including boron-neutron capture therapy (BNCT). In this paper, we present the results of boron-rich compound (carborane borate) attachment to previously aminated by (3-aminopropyl)-trimethoxysilane (APTMS) iron oxide NPs. Fourier transform infrared spectroscopy with Attenuated total reflectance accessory (ATR-FTIR) and energy-dispersive X-ray analysis confirmed the change of the element content of NPs after modification and formation of new bonds between Fe₃O₄ NPs and the attached molecules. Transmission (TEM) and scanning electron microscopy (SEM) showed Fe₃O₄ NPs’ average size of 18.9 nm. Phase parameters were studied by powder X-ray diffraction (XRD), and the magnetic behavior of Fe₃O₄ NPs was elucidated by Mössbauer spectroscopy. The colloidal and chemical stability of NPs was studied using simulated body fluid (phosphate buffer—PBS). Modified NPs have shown excellent stability in PBS (pH = 7.4), characterized by XRD, Mössbauer spectroscopy, and dynamic light scattering (DLS). Biocompatibility was evaluated in-vitro using cultured mouse embryonic fibroblasts (MEFs). The results show us an increasing of IC₅₀ from 0.110 mg/mL for Fe₃O₄ NPs to 0.405 mg/mL for Fe₃O₄-Carborane NPs. The obtained data confirm the biocompatibility and stability of synthesized NPs and the potential to use them in BNCT.