Patients with spinal cord injury (SCI) experience a high osteoporosis incidence, which increases fracture risk. Recently, a sclerostin antibody was introduced as a target biomarker to treat osteoporosis. We aimed to determine the serum concentration of sclerostin and factors affecting its concentration over time. This was a prospective cross-sectional study. The inclusion criteria were (1) SCI patients with a grade 3 modified functional ambulatory category score (FAC—patients requiring firm continuous support) and (2) patients whose injury occurred >1 month ago. The exclusion criterion was a history of osteoporosis medication administration within 6 months. The collected data included bone biomarkers (carboxy-terminal collagen crosslinks (CTX), procollagen type 1 intact N-terminal propeptide, and sclerostin), clinical data (FAC, lower extremity motor score), body mass index, SCI duration, and hip bone mineral density (BMD). This study recruited 62 patients with SCI. Sclerostin levels significantly correlated with age, CTX level, and hip BMD. SCI duration was negatively correlated with sclerostin levels. Lower extremity motor scores were not significantly correlated with sclerostin levels. The acute SCI state showed a higher sclerostin level than the chronic SCI state. Sclerostin showed a significant relationship with CTX. In conclusion, age and BMD affect sclerostin concentration in patients with SCI.