In pediatric Crohn's disease (CD) patients, it is important to define the disease phenotype at diagnosis for stratifying risk. In this retrospective study, we aimed to assess the disease phenotype compared to EUROKIDS registry and analyze disease outcome of pediatric CD patients according to upper gastrointestinal (GI) tract involvement. A total of 312 patients were included. The median age at diagnosis was 13.7 years and 232 patients (74.4%) were identified to have upper GI involvement at diagnosis. In Korean pediatric CD patients, there were significant differences in male predominance (72.8% vs. 59.2, p < 0.001), proportion of upper GI involvement (74.4% vs. 46.2%, p < 0.001), and perianal disease (62.1% vs. 8.2%, p < 0.001) compared to data in the EUROKIDS registry. Younger age (OR 2.594, p = 0.0139) and ileal involvement (OR 2.293, p = 0.0176) at diagnosis were associated with upper GI involvement. There were no significant differences in disease outcomes between patients with and without upper GI tract involvement. This study revealed that upper GI involvement is more prevalent in Korean patients with pediatric Crohn's disease than in European patients, and the disease outcome did not appear to differ according to upper GI tract involvement.