Tumor necrosis factor α (TNF‐α)‐induced osteoclast formation have been demonstrated to play an important role in the pathogenesis of estrogen deficiency‐mediated bone loss, but the exact mechanisms by which TNF‐α enhanced osteoclast differentiation were not fully elucidated. The class III semaphorins members were critical to regulate bone homeostasis. Here, we identified a novel mechanism whereby TNF‐α increasing Semaphorin3D expression contributes to estrogen deficiency‐induced osteoporosis. In this study, we found that Semaphorin3D expression was upregulated by TNF‐α during the process of RANKL‐induced osteoclast differentiation. Inhibition of Semaphorin3D in pre‐osteoclasts could attenuate the stimulatory effects of TNF‐α on osteoclast proliferation and differentiation. Mechanistically, blocking of the Jun N‐terminal kinase (JNK) signaling markedly rescued TNF‐α‐induced Semaphorin3D expression, suggesting that JNK signaling was involved in the regulation of Semaphorin3D expression by TNF‐α. In addition, silencing of Semaphorin3D in vivo could alleviate estrogen deficiency‐induced osteoporosis. Our results revealed a novel function for Semaphorin3D and suggested that increased Semaphorin3D may contribute to enhanced bone loss by increased TNF‐α in estrogen deficiency‐induced osteoporosis. Thus, Semaphorin3D may provide a potential therapeutic target for the treatment of estrogen‐deficiency induced osteoporosis. We found that TNF‐a could increase Sema3D expression in RANKL‐induced osteoclast formation. Upregulation of Sema3D expression was required for TNF‐a‐mediated osteoclast proliferation and differentiation. JNK signaling was involved in the regulation of Sema3D expression by TNF‐a.