Conducting clinical trials is often complex and involves many individuals from a variety of services, each with a specific role in ensuring its successful implementation. Although an experienced clinical trialist may anticipate many of the challenges, others may be unexpected and detrimental to the successful completion of a study. We describe the use of simulation during preparation for initiation of a randomized clinical trial of a new preparation of antiseizure medication in neonates with seizures. The process of identification of stakeholders and roles, scenario development, and identification of challenges are described. Lessons learned included the potential benefits of simulation exercises, simulation challenges, and challenges associated with the study itself. We posit that going through the steps of a study, rather than merely reading them from a manual of procedures, will help identify potential barriers, complexities, and contingencies that are not readily apparent and may result in fewer protocol deviations and violations.