Pfeiffer syndrome is a pleiotropic disorder characterized by multiple suture craniosynostosis, broad and medially deviated thumbs and great toes, and variable cutaneous syndactyly. We present the case of a 16-month-old boy with Pfeiffer syndrome type 2 who presented with intestinal malrotation for which the diagnosis was delayed. This is a rare complication of Pfeiffer syndrome, with few reported cases in the literature. This case illustrates the importance of recognizing gastrointestinal malrotation as a possible cause of feeding intolerance and persistent vomiting in patients with the severe forms of Pfeiffer syndrome.