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Objectives: Ghana's quest to reduce neonatal mortality, in hospital facilities and communities, continues to be a nightmare. The pursuit of achieving healthy lives and well-being for neonates as enshrined in Sustainable Development Goal three lingered in challenging hospital facilities and communities. Notwithstanding that, there have been increasing efforts in that direction. This study examines the contributing factors that hinder the fight against neonatal mortality in all hospital facilities in the Sunyani and Sunyani West Municipal Assemblies in Bono Region, Ghana. Methods: The study utilized neonatal mortality data consisting of neonatal deaths, structural facility related variables, medical human resources, types of hospital facilities and natal care. The data was collected longitudinally from 2014 to 2019. These variables were analysed using the negative binomial hurdle regression (NBH) model to determine factors that contribute to this menace at the facility level. Cause-specific deaths were obtained to determine the leading causes of neonatal deaths within health facilities in the two municipal assemblies. Results: The study established that the leading causes of neonatal mortality in these districts are birth asphyxia (46%), premature birth (33%), neonatal sepsis (11%) and neonatal jaundice (7%). The NBH showed that neonatal mortality in hospital facilities depend on the number of incubators, monitoring equipment, hand washing facilities, CPAPb machines, radiant warmers, physiotherapy machines, midwives, paediatric doctors and paediatric nurses in the hospital facility. Conclusions: Early management of neonatal sepsis, birth asphyxia, premature birth and neonatal infections is required to reduce neonatal deaths. The government and all stakeholders in the health sector should provide all hospital facilities with the essential equipment and the medical human resources necessary to eradicate the menace. This will make the realization of Sustainable Development Goal three, which calls for healthy lives and well-being for all, a reality. [ABSTRACT FROM AUTHOR]