The causes of intractable diarrhoea in infancy are varied, and can be classified into enteropathic and non-enteropathic groups. Congenital tufting enteropathy (CTE) is a rare cause of enteropathic form of intractable diarrhoea in infants requiring nutritional supplementation. We herein report a case of CTE in a one-year-old female child who presented with recurrent abdominal distension, frequent watery diarrhoea and marked stunted growth soon after birth. A systematic clinical, laboratory and pathological evaluation brought out the etiology, followed by genotypic confirmation. Histological examination revealed mild villous abnormality with presence of epithelial tufts both in the villous and crypt surface, in the duodenum and rectal biopsies supported by complete loss of MOC31 staining. Deep sequencing revealed homozygous 3' splice mutation at intron 5 of the EPCAM gene (c.556-14A>G). She was given TPN support and discharged with weight gain under home-based parenteral nutrition supplement. This case brings out the need for a multidisciplinary team approach to reveal underlying the cause of infantile intractable diarrhoea and report a favorable outcome with nutritional supplementation.