Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is primarily manifested by persistent inflammation affecting the musculoskeletal system and the skin. The treatment of SAPHO syndrome remains a challenge. Tofacitinib is a Janus kinase (JAK) inhibitor that inhibits a range of cytokines. Here, we report a patient who had been diagnosed with SAPHO syndrome refractory to initial treatment and responded well to tofacitinib. An 18-year-old male was presented to our center with polyarthritis, associated with sternal and clavicular pain. There was a nine-month history of skin lesions affecting his chest and back and was diagnosed with a case of SAPHO syndrome. Nonsteroidal anti-inflammatory drugs, conventional disease-modifying antirheumatic agents, and biological drugs were unhelpful. After five weeks of starting tofacitinib at 5mg twice daily in combination with methotrexate, the patient reported significant improvement in dermatological and osteoarticular symptoms. JAK inhibitors, especially tofacitinib, can be a good choice for the treatment of SAPHO refractory to disease-modifying antirheumatic drugs (DMARDs) and tumor necrosis factor (TNF) inhibitors.