Neonatal mortality is a vital indicator of healthcare system effectiveness. In 2019, provincial Neonatal Mortality Rates (NMRs) in Iran ranged from 3.1 (2.6–3.7) to 10.0 (9.2–10.8) per 1,000 live births, illustrating significant regional disparities. Despite these concerning figures, the transfer of critically ill neonates to obtain necessary medical interventions has received insufficient attention, revealing a critical gap in healthcare services. This study aimed to gather stakeholder perspectives on neonatal transfer in Tehran, elucidate the obstacles encountered in neonatal transport logistics, and outline the operational framework underlying these transfers. A qualitative descriptive design was employed, involving semi-structured interviews across five prominent hospitals in Tehran Province (N = 5, n = 5). Participants (N = 6, n = 37) included key stakeholders—such as neonatologists, NICU staff, emergency personnel, and parents—who shared first-hand experiences in the transfer of critically ill infants. A pilot-tested questionnaire guided discussions on various aspects of the transport process, including coordination, infrastructure, team readiness, and equipment availability. As the first study in Iran to comprehensively map the logistical and operational challenges associated with neonatal transport, the findings reveal multiple transfer modes—private vehicles, ambulances, and air transport—and the unique barriers each presents. These challenges fall into five main categories: Infrastructure, Systemic Issues, Communication, Team awareness, and Equipment. Taken together, they underscore systemic inefficiencies that compromise timely and safe transfers for neonates in critical condition.