Cystic echinococcosis (CE) is a cosmopolitan parasitic disease caused by Echinococcus granulosus. We aimed to assess the epidemiological aspects of the disease in hospitalized children from Western Romania, a well-known endemic area for CE. We retrospectively investigated the medical records of children hospitalized between 1998 and 2022. A total of 144 patients were included, and 58.3% were from rural areas. The number of cases increased with age, from 9% in the age group 3–5 years to 59.7% in the age group 11–17 years. The liver was more frequently affected (65.3%), and a significant association between gender and the affected organ was noted; liver cysts were more frequently diagnosed in girls, while lung cysts were recorded mostly in boys. Complications were more frequently reported in patients with pulmonary CE compared to hepatic CE (p = 0.04). Boys had more complications (16/23, 69.6%) compared to girls (7/23, 30.4%) (p = 0.03). A third of the children were hospitalized for more than 14 days, and multiple hospitalizations were recorded in 31.3% of the patients. This paper provides new insights into the epidemiologic features of cystic echinococcosis in children from Western Romania. Our findings indicate that exposure to the parasite starts in childhood, and the rate of hospitalization increases with age. Public health strategies should be implemented and permanently improved in order to lower the prevalence of CE in children.