Juvenile systemic lupus erythematosus (JSLE) and autoimmune hepatitis (AIH) are both autoimmune disorders that are rare in children and have a widespread clinical manifestation. A few case reports have shown a JSLE-AIH associated disorder. To our knowledge, this is the first study that simultaneously evaluated the prevalence of JSLE-AIH in a large JLSE and AIH population in groups of Hepatology and Rheumatology of a tertiary Paediatric University Hospital. In a 24-year period, 228 patients were diagnosed with JSLE (ACR criteria). In the same period, 252 patients were diagnosed with AIH according to the International Autoimmune Hepatitis Group. In this article, we present the demographic data, clinical features, laboratory exams and treatment of four children with both the diseases. The prevalence was 1.8% in JSLE population and was 1.6% in AIH population. The current median age was 15.5 years and three were females. In three of them, the diagnosis of AIH preceded JSLE. All of them had increased liver enzymes with a characteristic liver biopsy of AIH and responded to the combination of prednisone, azathioprine and antimalarial drugs. In conclusion, the presence of AIH-JSLE associated disorder was rarely observed. The liver biopsy could be necessary in patients with JLSE with a persistent increase of liver enzymes.