Purpose: Choledochal cysts are congenital anomalies that occur as localized cystic or fusiform dilatations of the biliary tree. Reflux and stasis of pancreatic enzymes in the biliary duct may relate to the development of intestinal metaplasia which might be an important factor related to the carcinogenesis of choledochal cyst, thus the expression of beta-catenin in the metaplastic epithelium might be associated with malignant transformation of choledochal cyst epithelium. Methods: This study was conducted at a tertiary care pediatric center between October 2014 and March 2017. Forty patients were evaluated for epithelial lining, mural ulceration, fibrosis, inflammation, and metaplasia. Results: Out of 40, 12 cases (30.0%) were the infantile age group and 28 cases (70.0%) were in the classic pediatric group. Ulceration was classified as grade 0 (14 cases, 35.0%), grade 1 (17 cases, 42.5%), or grade 2 (nine cases, 22.5%). Inflammation was classified as grade 0 (2 cases, 5.0%), grade 1 (26 cases, 65.0%), or grade 2 (12 cases, 30.0%). Fibrosis was classified as grade 0 (five cases, 12.5%), grade 1 (11 cases, 27.5%), grade 2 (17 cases, 42.5%), or grade 3 (seven cases, 17.5%). Metaplasia was noted in five (12.5%) out of 40 cases. All choledochal cysts with metaplasia showed beta-catenin nuclear positivity on immunohistochemistry and were followed up. Conclusion This study emphasizes the importance of detailed histopathological examination and documentation of metaplastic changes. Metaplasia was associated with beta-catenin nuclear positivity. These findings suggest a potential role for beta-catenin as a marker of metaplastic changes in choledochal cysts.