Background: Lysinuric protein tolerance (LPI) is a rare autosomal, recessive, metabolic disease caused by mutations in the SLC7A7 gene. It was first reported in the Finnish population in 1965, and involved multiple organ systems like the digestive, blood, respiratory, nervous, urinary and other systems, due to a defect in the transport of the dialkylamino acid plasma membrane. Case presentation: A girl with severe malnutrition, underdevelopment and a long-term history of hepatosplenomegaly, presented with recurrent fever, cough and shortness of breath. Computer tomography (CT) revealed that she had a considerable lung infection, and the results of laboratory tests showed that she had moderate anemia. The maximum value of type B natriuretic peptide (BNP) was 6076 ng/L (0-300). In this course, the blood ammonia was 85.5 μmol/L (11-40), the serum ferritin was 3827 ng/mL (10-120), the complement 3 was 237 mg/L (790-1520), complement 4 was 53.1 mg/L (100-400), the titre of anti-nuclear antibody (ANA) was 1:320 and the anti-dsDNA antibody was positive. The patient died of severe pneumonia at 5 years old. A genetic test indicated that the patient’s SLC7A7 gene had a compound heterozygous mutation, including c.724T>C chr14-23248048 p.W242R and c.719C>T chr14-23248053 p.S240L, inherited from the patient’s father and mother, respectively. Conclusions: The patient was diagnosed with LPI with systemic lupus erythematosus (SLE), and severe pneumonia, and her SLC7A7 gene had a compound heterozygous mutation.