Many decisions related to the marketing authorisation of medicinal products as well as decisions for processes such as Health Technology Assessment (HTA), reimbursement and pricing of medicines, and the setting of clinical guidelines, are taken in the face of significant uncertainties. Moreover, decision-making can be impacted by biases resulting from psychological heuristics. In other domains where decisions have to be taken with imperfect or incomplete evidence, Structured Expert Judgement (SEJ) has been found to be useful in making the best use of available evidence, and synthesising it with professional expertise, stakeholders’ values and concerns. To date, formal SEJ has only been used to a limited extent in healthcare. Aspects affecting decisions for marketing authorisation and health technology assessment, reimbursement and pricing of medicines are described and the main risks and uncertainties are identified. Some considerations and recommendations for the use of SEJ to strengthen these decisions are made.