AbstractThe dental pulp is a highly innervated tissue transmitting pain‐related sensations in the tooth. Consequently, understanding the intricacies of its innervation mechanism in odontogenesis is crucial for gaining insights into dental pain and developing dental pain‐modulating agents. This study examined neuroregulatory molecules such as neurotrophic factors (nerve growth factor [NGF], brain‐derived neurotrophic factor [BDNF], neurotrophin‐4 [NTF‐4], and neurturin [NRTN]) and neuroinhibitory factors (slit2, ephrin isoforms and netrin‐1) in developing rat teeth with follicles. NGF, BDNF and NRTN transcriptions showed time‐dependent upregulation, particularly during the root formation stage. In contrast, NTF‐4 mRNA was highly expressed at the cap stage, but became downregulated over time. Slit2 and ephrin‐B2 expression was distinct at the cap stage and then downregulated in a time‐dependent manner. Ephrin‐A5 and netrin‐1 expression did not significantly change. Immunofluorescence analysis revealed a robust expression of both ephrin‐B2 and slit2 in the outer and inner dental epithelia of the enamel organ, a non‐neurogenic tissue, during the cap stage of 3rd molar germs. In contrast, BDNF was predominantly localized in dental papilla cells and odontoblasts during the root formation stage. These results suggest that neuroregulatory molecules, such as BDNF, slit2 and ephrin‐B2, may be important in identifying therapeutic targets for modulating dental pulp pain.