An increasing number of clinical guidelines are being developed to provide high-quality and consistent standards of care, most of which are based on a specific diagnosis. In a pediatric emergency department, the diagnosis may not be known on presentation and the junior doctors are usually the first to assess a patient and will need to establish the diagnosis and execute a management plan. In these circumstances, problem-based guidelines are useful to clinicians and provide a decision pathway by which a clinician can develop a working diagnosis and then follow a guideline for the particular disease. More experienced clinicians may find guidelines for individual diseases or conditions to be of more use. High-quality evidence for either of these styles of guidelines is not readily available and may require extrapolation from the literature focusing on adults or a consensus approach to inform discussions and the development of the recommendations. Due to the complexity of the process it must be systematic, transparent and open to scrutiny. The cost of developing a guideline in a systematic transparent process is high and it is, therefore, essential to ensure the implementation of the guidelines with as much rigor as the development itself. This review discusses the challenges encountered while developing and implementing pediatric emergency guidelines and concludes with the authors' suggestions for future research in this area.