Cat scratch disease (CSD) is an infectious disease caused by Bartonella henselae. Atypical clinical presentations of CSD include prolonged fever and multiple hepatosplenic lesions, although these are rare. Furthermore, multiple renal lesions are extremely rare in CSD. The patient was an 11-year-old Japanese girl who had a prolonged fever of unknown cause after being scratched and bitten by a kitten. Abdominal computed tomography (CT) revealed multiple small, round hypodense lesions in both kidneys and in the spleen. Based on her history and the results of CT, a diagnosis of CSD was made; the diagnosis was confirmed with serological tests, which indicated antibodies against Bartonella henselae. After treatment with azithromycin, her fever immediately improved. Careful history taking and imaging are essential for the diagnosis of atypical CSD. In CT images, not only hepatosplenic lesions but also renal lesions are important features indicative of a diagnosis of atypical CSD. Subsequently, a diagnosis of CSD can be confirmed with specific serological tests. To the best of our knowledge, this is the first reported Japanese case of multiple renal and splenic lesions in a patient with CSD. Although atypical CSD is difficult to diagnose, an early diagnosis is important to prevent invasive examinations.