Ceria (CeO$_2$) nanoparticles are known to be very often used in various applications from biomedicine to fuel cells. To optimize the applications, detailed information about the physicochemical properties such as size, shape, and charge of nanoparticles should be available. Therefore, in our study we performed a systematic study of ceria nanoparticles ranging from synthesis to comprehensive experimental and theoretical characterization. We synthesized ceria nanoparticles using two synthesis paths which led to the formation of two types of ceria nanoparticles. The structure and charging properties of both types of ceria nanoparticles were studied by using X-ray powder diffraction (XRD), high-resolution transmission electron microscopy (HR-TEM), particle charge detector (PCD) for surface charge density, and a ZetaPlus instrument for electrophoretic mobility measurements. The results suggested that in the case where hydrolysis of Ce(NO$_3$)$_3$ at room temperature was applied nanoparticles with morphology close to a spherical, more exactly truncated octahedron were synthesized. On the other hand, nanoparticles obtained by hydrothermal synthesis had characteristic cube-like morphology. Finally, for more complete understanding and interpretation of the studied system, we prepared a theoretical model based on the classical density functional theory for electrolyte solutions coupled with the surface charge regulation via the law of mass action. Even without using fitting parameters, the theory adequately describes the experimental data. All the results obtained in our study could serve as a basis for obtaining tuned and engineered ceria nanoparticles with optimized physicochemical properties which could lead to the improved applications of the nanotechnology in the biomedical research.