Abstract Background Kikuchi–Fujimoto disease is an uncommon systemic disease that mostly affects young women. Kikuchi–Fujimoto disease typically manifests as necrotizing lymphadenopathy, which frequently follows by a fever; however, Kikuchi–Fujimoto disease occurs rarely in extranodal regions. One of the most important accompaniments of Kikuchi–Fujimoto disease is its connection with autoimmune diseases such as systemic lupus erythematosus. This case presents a simultaneous occurrence of Kikuchi–Fujimoto disease with liver involvement and systemic lupus erythematosus in a young female patient. Case presentation We present a rare case of a 20-year-old white woman who presented with fever, joint pains, myalgia, and shortness of breath. Initial hospitalization and treatment for fever of unknown origin did not yield improvement. Physical examination revealed cervical and supraclavicular lymphadenopathy, and laboratory investigations showed abnormal blood counts, elevated inflammatory markers, and positive autoimmune serologies. Imaging studies revealed bilateral pleural effusion and liver lesions. Lymph node biopsy confirmed the diagnosis of Kikuchi–Fujimoto disease, and liver biopsy showed extranodal involvement. The patient was diagnosed with Kikuchi–Fujimoto disease-associated systemic lupus erythematosus and treated with hydroxychloroquine and corticosteroids. The patient showed gradual resolution of symptoms and lymphadenopathy with treatment. Conclusion Kikuchi–Fujimoto disease is a rare systemic condition primarily impacting young females. It is characterized by necrotizing lymphadenopathy, often accompanied by fever. Although Kikuchi–Fujimoto disease is predominantly seen in the lymph nodes, occurrences in non-nodal areas are infrequent. When diagnosing Kikuchi–Fujimoto disease, it is essential to screen patients for systemic lupus erythematosus. In this particular case, we observed liver involvement along with the presence of both Kikuchi–Fujimoto disease and systemic lupus erythematosus.