Background: General practitioners (GP) report multiple challenges when treating individuals with intellectual disabilities which may influence referral rates. The study aimed to establish factors that influence GP's decision-making when referring a child with intellectual disabilities to the emergency department. Method: Discrete choice experiments (DCEs) are increasingly used in health research to further understand complex decision making. A DCE was designed to assess the relative importance of factors that may influence a GP's (N = 157) decision to refer. Results: A random parameters model indicated that perceived limited parental capacity to manage an illness was the most important factor in the decision to refer a child to the ED, followed by a repeat visit, a referral request from the parent, and a Friday afternoon appointment. Conclusion: Understanding the factors that influence referral is important for service improvement and to strengthen primary care provision for this population and their families.