This study aimed to examine the contributions of brain-derived neurotrophic factor (BDNF) at the injury site toward neuroma formation and nerve regeneration after inferior alveolar nerve transection. Histological analysis confirmed neuroma formation at 2 weeks after complete transection of the inferior alveolar nerve. A local administration of an antibody to BDNF inhibited connective tissue proliferation at the injury site and promoted nerve fiber integrity. Fluorogold labeling showed a significantly higher number of labeled cells in the trigeminal ganglion in the anti-BDNF-treated group compared with the vehicle control group. In-situ hybridization histochemistry showed intense signals for tropomyosin receptor kinase B mRNA in the area of the injury site containing fibrous or granular tissue in the anti-BDNF-treated group. In contrast, these signals were close to the detection limit in the area of the perineurium in intact nerve trunks, indicating that the signals were expressed by fibroblasts within the connective tissue. These findings suggest that antagonization of endogenous BDNF induced by nerve injury reduces neuroma formation, without inhibiting damaged axon regeneration.