In this study, we attempted to develop a dental caries prevention method using a bioapatite (BioHap), an eggshell-derived apatite with nanoparticle size and biocompatibility, with a high-concentration fluoride tooth surface application method. The enamel acid resistance after the application of the proposed method was compared with that of a conventional topical application of fluoride using bovine tooth enamel as an example. The tooth samples were divided into three groups based on the preventive treatment applied, and an acid challenge was performed. The samples were evaluated for acid resistance using qualitative and quantitative analytical methods. The BioHap group demonstrated reduced enamel loss and improved micro-Vickers hardness, along with a thick coating layer, decreased reaction area depth, and decreased mineral loss value and lesion depth. The combination of BioHap with high-concentration fluoride led to the formation of a thick coating layer on the enamel surface and better suppression of demineralization than the conventional method, both qualitatively and quantitatively. The proposed biocompatible nano-hydroxyapatite coating method is expected to become a new standard for providing professional care to prevent dental caries.