Rising costs of innovative drugs and therapeutics (D&Ts) have led to resource allocation challenges for healthcare institutions. There is limited evidence to guide priority-setting for institutional funding of high-cost D&Ts. This study sought to identify and elaborate on the substantive principles and procedures that should inform institutional funding decisions for high-cost off-formulary D&Ts through a case study of a quaternary care paediatric hospital. Semi-structured, qualitative interviews, both virtual and in-person, were conducted with institutional stakeholders (i.e. staff clinicians, senior leadership, and pharmacists) (n = 23) and two focus groups at The Hospital for Sick Children in Toronto, Canada. Participants involved in, and impacted by, high-cost off-formulary drug funding decisions were recruited through stratified, purposive sampling. Participants were approached for study involvement between July 27, 2020 and June 7, 2022. Data was analysed through reflexive thematic analysis. Institutional resource allocation for high-cost D&Ts was identified as ethically challenging but critical to sustainable access to novel therapies. Important substantive principles included: 1) clinical evidence of safety and efficacy, 2) economic considerations (direct costs, opportunity costs, value for money), 3) ethical principles (social justice, professional/organizational responsibility), and 4) disease-specific considerations. Multidisciplinary deliberation was identified as an essential procedural component of decision-making. Participants identified tension between innovation and the need for evidence-based decision-making; clinician and institutional responsibilities; and value for money and social justice. Participants emphasized the role of health system-level funding allocation in alleviating the financial and moral burden of decision-making by institutions. This study identifies values and processes to aid in the development and implementation of institutional resource allocation frameworks for high-cost innovative D&Ts.