Chronic enteropathy associated with the SLCO2A1 gene (CEAS) is a rare, autosomal recessive disorder characterized by multiple chronic ulcerative and structuring lesions in the small intestine, primarily affecting the ileum. It often presents with symptoms of chronic blood loss and protein loss, including iron deficiency anemia and abdominal pain, similar to other nonspecific small bowel enteropathies. This case report describes a 15-year-old boy with a 10-year history of recurrent abdominal pain, melena, anemia, and hypoalbuminemia. Initial clinical, endoscopic, and radiological findings suggested inflammatory bowel disease, which led to trials of various therapies, including corticosteroids, antivirals, and biologicals, with incomplete remission. Molecular analysis identified a homozygous SLCO2A1 gene mutation, confirming CEAS. Histopathology revealed extensive mucosal ulceration and submucosal fibrosis in the ileum, with repeat biopsies showing chronic inflammation and villous atrophy. The case underscores the need for comprehensive clinical, histopathological, and molecular evaluation in pediatric patients presenting with chronic nonspecific small bowel ulcers to ensure accurate diagnosis and management of CEAS. This report also adds to the limited global literature on CEAS, being the first documented case in India with a unique exon 11 mutation in SLCO2A1, contributing to the understanding of disease heterogeneity in non-consanguineous populations.