The number of expensive drugs for rare diseases (EDRDs) approved by Health Canada and their contribution to healthcare costs have been rapidly increasing. The federal government has announced a three-year funding commitment of $1.4 billion for EDRDs, but principles need to be developed for how that funding will be allocated, especially in cases where insufficient data are available to guide decision making. Here, we review the role of evidence quality in making choices and draw on the experience from other countries to put forward five principles about how the money should be spent.