Background: The clinical manifestations of Epstein-Barr virus (EBV) infection are usually infectious mononucleosis, chronic active EBV infection, and related hemophagocytic lymphohistiocytosis. The incidence of non-calculous cholecystitis in children is not high, and non-calculous cholecystitis in children caused by EBV infection remains a rarity, which is often overlooked in clinical practice. The purpose of this study was to describe the clinical characteristics, laboratory tests, imaging findings, and treatment outcomes of a 9-year-old boy. Case Description: This case details a 9-year-old boy who was diagnosed with infectious mononucleosis, acute non-calculous cholecystitis (ACC), and severe hepatic insufficiency. ACC is very rare in pediatric patients, especially because of its own liver function impairment, which is easily overlooked in clinical diagnosis. At the beginning of the disease, the patient presented with upper abdominal pain and vomiting, which was misdiagnosed as acute gastroenteritis, and later with fever, yellowing of the skin, dark yellow urine, repeated abdominal pain and vomiting, and serious liver damage, which was later found to be accompanied by ACC. After receiving regular treatment, the patient's condition improved, with no discomfort reported in the follow-up six months and one year thereafter. This case emphasizes that the clinical work should be carefully performed, in order not to miss any specific clinical manifestations. In this study, we highlight a new problem posed by EBV infection, as well as early awareness of rare cases of ACC in children caused by EBV infection. Conclusions: This case report provides a new supplement for the diagnosis and treatment of rare non-calculous cholecystitis in children caused by EBV infection, and provides a clinical basis for young pediatricians to make a timely diagnosis, reduce misdiagnosis, and prevent missed diagnosis.