Lemierre syndrome develops in healthy young patients as a result of bacteremia after oral cavity infection. It causes thrombophlebitis in the internal jugular vein. Infection can easily occur during immunosuppressive treatment in patients with systemic lupus erythematosus and become severe. We present a case of Lemierre syndrome in a patient with systemic lupus erythematosus. A 56-year-old woman presented with fever, left lower toothache, and skin symptoms from the left neck to the anterior chest. Clinical presentation and laboratory investigations revealed Lemierre syndrome. The inflammation and thrombus disappeared with antibiotic and anticoagulant therapies. However, transient hypocomplementemia and elevated antinuclear antibody levels were observed during treatment; therefore, a concomitant systemic lupus erythematosus flare was considered. In systemic lupus erythematosus patients with Lemierre syndrome, complement and antinuclear antibody levels are modified, so other indicators should be precisely evaluated, such as levels of urinary protein, sediment, serum creatinine and anti-dsDNA antibody, and systemic lupus erythematosus disease activity index.