Semaphorin 3A (Sema3A), characterized by a conserved N-terminal "Sema" domain, was originally described as an axon guidance molecule. Recent research indicates that it performs a critical function in the skeletal system. This review highlights recent advances in understanding of the role of Sema3A in the skeletal system as a regulator of bone metabolism and as a potential drug target for bone disease therapy. We summarize Sema3A functions in osteoblastogenesis and osteoclastogenesis, as well as in innervation, and we discuss its multifunctional role in various bone diseases such as osteoporosis and low back pain. Despite limited research in this field, our aim is to promote further understanding of the function of Sema3A in the skeletal system.