Emphysematous osteomyelitis (EO) is a rare and dangerous infection characterized by the presence of intraosseous gas. In this case report, a 65-year-old man with primary central nervous system lymphoma had recurrent infections and pain in his shoulders. Urine and blood cultures revealed Klebsiella pneumoniae. CT showed the formation of gas in the right humerus and left clavicle penetrating the surrounding tissues, which led to the diagnosis of EO. After several long-term antibiotic treatments, the patient underwent surgery on the right proximal humerus. Biopsy cultures revealed K. pneumoniae.