BackgroundIran’s fee-for-service (FFS) payment model in neonatal intensive care units (NICUs) is contentious due to the involvement of multiple stakeholders with differing interests, leading to increased costs, fragmentation, and reduced quality of care. This study explores the experiences and challenges of stakeholders with the NICU payment system and considers alternative payment methods.MethodA qualitative research approach was used, involving key informant interviews with stakeholders at various levels of the health system. Data were collected between March 2022 to September 2023 using a purposive sampling method with a snowball strategy. The transcribed data were analyzed using an inductive thematic approach in MAXQDA, with themes and sub-themes emerged and assessed by two independent coders. Four trustworthiness criteria were applied to ensure the quality of the results.ResultsThe study involved 23 participants with diverse NICU payment backgrounds, identifying issues related to service accessibility, rising costs, neonatologists’ income, and service quality. Stakeholders held differing views on the best payment model: health insurance executives favored a prospective payment method, faculty members favored supported modified FFS or per diem, and neonatal specialists expressed concerns about low tariffs and delayed payments.ConclusionIran’s NICU payment system is unsatisfactory and requires urgent reform. Although stakeholders disagree on the best approach, reforms must be evidence-based and collaborative, addressing structural and cultural issues within the health system. The identification of an optimal payment system is essential for supporting neonatal care, benefiting newborns, families, society, and the broader health system.