Pyomyositis may mimic deep vein thrombosis and be misdiagnosed in patients with systemic lupus erythematosus (SLE). We report here on patient with SLE with severe thoracic pyomyositis presented with right upper arm swelling and fever. The patient fully recovered after a serial surgical debridement and antibiotic therapy. Pyomyositis, as well as deep vein thrombosis, should be considered during the differential diagnosis of patients with SLE experiencing fever and unilateral limb oedema. CT and identification of causal pathogens are crucial in the diagnosis of pyomyositis. Early effective antibiotic treatment as well as surgical intervention can together bring about a better outcome.