•The SOX9 expression increased in tumor tissues and peripheral blood of malignant and benign bone tumors.•The protein level of SOX9 is enhanced in malignant bone tumor tissues.•SOX9 over-expression correlated with tumor severity, grade, invasion feature, poor response to therapy, and recurrence. The status of the local and circulating SOX9, a master regulator of the tumor fate, and its relevance to tumor types, severity, invasion feature, response to therapy, and chemotherapy treatment were surveyed in bone cancer in the current study. The SOX9 expression level was evaluated in tissue and peripheral blood mononuclear cells from patients with different types of malignant and benign bone tumors also tumor margin tissues using Real-Time PCR. The protein level of SOX9 was assessed using immunohistochemistry and western blot analysis. Also, the correlations of the SOX9 expression level with the patient’s clinical and pathological features were considered. The remarkable overexpression of SOX9 was detected in bone tumors compared to tumor margin tissues (P < 0.0001). Malignant bone tumors revealed a higher expression of SOX9 compared to benign tumors (P < 0.0001) while osteosarcoma tumors showed higher expression levels compared to Ewing sarcoma, and chondrosarcoma. Overexpression of SOX9 was observed in high grade, metastatic, recurrent tumors also tumors with poor response to therapy. Besides, the patients under the chemotherapy treatment demonstrated higher levels of SOX9 compared to the rest of malignant tumors (P = 0.02). The simultaneous up-regulation of circulating SOX9 in the patients with bone cancer was observed compared to healthy individuals (P < 0.0001) accompanying with overexpression of SOX9 in malignant tumors compared to benign tumors (P < 0.0001). The circulating SOX9 expression was up-regulated in the patients with malignant bone tumors who receive chemotherapy treatment also patients with high grade, metastatic, recurrent tumors. The protein level of SOX9 was in line with our data on the SOX9 gene expression. The simultaneous overexpression of local and circulating SOX9 in bone cancer besides its positive correlation with tumor severity, malignancy, size, and chemotherapy may deserve receiving more attention in bone cancer diagnosis and therapy.