Designing clinical trials in rare diseases comes with a specific set of challenges including limited knowledge around the natural history of a disease, small sample size available for trial participation, regulatory guidance that is not calibrated to the rare disease context, manufacturing and supply issues, and safety and financial risks. Here, we discuss some of these potential challenges and how, through proactive early engagement with key opinion leaders, regulatory bodies, and patient groups, a cohesive and strategic clinical development plan can be created to provide the strongest foundations when marketing approval is sought. Medical Writing. 2023;32(1)54-57. https://doi.org/10.56012/cwaa8066