Synovitis, acne, pustulosis, hyperostosis, osteitis (SAPHO) syndrome is a rare inflammatory condition associated with inflammatory bowel disease. Limited data exist on standardized management. We report a case of refractory SAPHO syndrome and ulcerative colitis (UC) treated successfully with tofacitinib. A 54-year-old man with UC presented with an intractable headache. A diagnosis of SAPHO syndrome was made based on the finding of sterile osteitis in the skull base and persistent severe UC. Symptoms, imaging, and endoscopy revealed persistent UC and osteitis despite multiple therapies. Tofacitinib was initiated and clinical remission was achieved. Tofacitinib is an effective treatment of refractory inflammatory bowel disease and SAPHO syndrome.