Medical advancement has increased the confidence in successful organ transplants in end-stage patients. As the waitlist of organ demand is multiplying, the organ allocation process is becoming more crucial. In this situation, a transparent and efficient organ allocation policy is required. This study evaluates the preferences of medical experts to substantial factors for allocating organs in different hypothetical scenarios. Twenty-five medical professionals with a significant role in organ allocation were interviewed individually. The interview questionnaire comprised demographic information, organ donation status, important organ allocation factors, public preference knowledge, and experts’ preferences in different hypothetical scenarios. Most medical experts rated the waiting time and prognosis as the most important, while the next of kin donor status and care and contribution to the well-being of others were the least important factors for organ allocation. In expert opinion, medical experts significantly considered public preferences for organ allocation in making their decisions. Altogether, experts prioritized waiting time over successful transplant, age, and donor status in the hypothetical scenarios. In parallel, less chance of finding another organ, donor status, and successful transplant were prioritized over age. Medical experts are the key stakeholders; therefore, their opinions are substantial in formulating an organ allocation policy.