Prolidase deficiency (PD) is an inherited disorder associated with cutaneous ulcers, intellectual disability, unusual facial appearance, skeletal deformities, hematological anomalies, splenomegaly, and chronic infections. We report a girl with PD who presented with early inflammatory bowel disease (IBD). A 2-month-old girl with a dysmorphic face presented with recurrent respiratory tract infections, vomiting, diarrhea and hepatosplenomegaly. She had steatorrhea, abnormal liver enzymes, hypergammaglobulinemia, autoantibody positivity and steatohepatitis in liver biopsy. On follow-up, skin lesions, pruritus and developmental delay were added. At the age of 21 months, IBD was diagnosed with persistent diarrhea, fever, hypoalbuminemia, elevated inflammatory markers, fecal leukocytes and aphthous ulcers in colon. Remission was achieved with prednisone and continued with mesalasine. Thrombocytopenia developed after 3 years. Her findings prompted us to further investigations. PD as the underlying molecular cause of the disease was detected by exome sequencing. In conclusion, PD should be considered in the differential diagnosis of some IBD patients.