We report a case of small bowel perforation from ileo-ileal intussusception with necrotising enterocolitis (NEC) after indomethacin exposure mimicking spontaneous intestinal perforation in an extremely preterm neonate. Indomethacin exposure can cause mesenteric hypoperfusion, resulting in an ischaemic lead point for intussusception and NEC. We advocate that intussusception should be considered as one of the differentials for neonates with recurrent feeding intolerance postindomethacin exposure. Diagnosis with early ultrasound by an experienced sonographer is crucial for timely surgical reduction to prevent intestinal perforation.