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Background The number of orphan drug approvals is currently increasing globally. This creates a significant burden on payers and healthcare systems. This study aimed to create a multi-criteria decision analysis (MCDA) tool for evaluating orphan drugs within the United Arab Emirates (UAE). The intended result of the tool is to provide evidence-based guidance to decision-makers in reimbursement and procurement decisions. Methods We conducted a literature search and local expert interviews to identify relevant preliminary criteria for the MCDA tool. Then we conducted a structured consensus-building session for healthcare experts and decision-makers in the UAE to develop the Emirati MCDA tool for orphan drugs. The experts voted for the criteria to be included in the tool and their ranking according to importance, as well as the weight of each criterion and its scoring function. To improve understanding and facilitate the voting process, experts were provided with a brief illustration of similar tools conducted in other countries before the voting sessions. Finally, the tool was developed in a Microsoft Excel sheet (Microsoft Corporation, Redmond, Washington, United States), and it was validated and tested based on real case studies, then it was fine-tuned accordingly based on the experts' discussions. The final tool was provided to the attendees to guide their decisions in the reimbursement and procurement of orphan drugs. Results The created tool provides a score for each analyzed orphan drug based on its value. Ten criteria were included in the final MCDA tool. These were cost-effectiveness (25.1% of the weight), magnitude of health gain (20.1%), availability of therapeutic alternative (14.3%), disease severity (11%), budget impact (7.9%), disease rarity (5.6%), strength of clinical evidence (5.6%), burden on households (4.5%), indication uniqueness (3.2%), and patients' age (2.6%). Conclusions Implementation of evidence-based healthcare necessitates assessing the fair value of each health technology. Addressing the high unmet medical needs and improving healthcare for patients with rare diseases are priorities within the UAE. The created Emirates MCDA tool for orphan drugs has the potential to help decision-makers implement value-based and evidence-based reimbursement decisions for orphan drugs., Competing Interests: The authors have declared financial relationships, which are detailed in the next section., (Copyright © 2024, Alnaqbi et al.)