Aphthous stomatitis is one of the side effects of chemotherapy and radiotherapy in cancer treatment. Rebamipide (RB) mouthwash for stomatitis acts as a radical scavenger. However, RB is poorly soluble in water, which leads to aggregation and precipitation of the dispersoid. The particle size of the drug needs to be less than 100 nm for the particles to reach the mucus layer in the oral cavity. In this study, we attempted to prepare nanoparticles of RB by cogrinding with polyvinylpyrrolidone (PVP) or hydroxypropyl cellulose (HPC) and sodium dodecyl sulfate (SDS) using a mixer ball mill, and evaluated the physicochemical properties of RB nanoparticles, the stability of dispersion in water, and permeation of the mucus layer in vitro. By cogrinding, the particle size decreased to around 110 nm, and powder X-ray diffraction (PXRD) of the particles showed totally broad halo patterns, which suggested a decreased crystalline region. Furthermore, the solubility of RB nanoparticles increased by approximately fourfold compared with RB crystals, and the water dispersibility and permeation of the mucus layer were improved. The results suggest that in a ternary ground mixture of RB, PVP or HPC, and SDS, the RB nanoparticles obtained can be applied as a formulation for stomatitis.