To develop a nanoscaled coating material for medical devices possessing weak antibacterial activity, dispersible and crystalline fluorinated hydroxyapatite (F-HAp) nanoparticles were prepared using antisintering agent to avoid calcination-induced sintering. The product was identical to fluorapatite, as determined by X-ray diffraction and Fourier transform infrared spectroscopy. The primary particles generally showed rod-shaped morphology with a length of 367 ± 67 nm and a width of 223 ± 21 nm measured by scanning electron microscopy (SEM). The dispersed average particle size (313 ± 51 nm) in ethanol analyzed by dynamic light scattering was almost the same as that obtained from the SEM images. In the evaluation of solubility in acidic aqueous solution, F-HAp and original hydroxyapatite (HAp) nanoparticles started to dissolve at around pH 3.4 and 4.2, respectively. Thus, the stability of F-HAp in a living body increased compared with original HAp. The antibacterial activity of F-HAp nanoparticles was higher than that of fluoride in sodium fluoride alone or the original HAp nanoparticles. However, it was estimated that the effect of F-HAp was much lower compared with that of silver, one of the popular antibacterial materials. Thus, the dispersed F-HAp nanoparticles possessing weak antimicrobial activity can be useful without severe damage to the living tissue.