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Introduction Balochistan is the largest of Pakistan's four provinces, yet it is also the poorest and most impoverished, particularly in terms of neonatal healthcare. In order to build and tailor strategies to improve neonatal outcomes, it is necessary to identify barriers and facilitators for interventions. Therefore, we conducted this study to provide an overview of neonatal healthcare quality and assess the structural capacity for the improvement and further development of neonatal healthcare facilities in Balochistan. Methods A descriptive, observational, cross-sectional study was conducted in Balochistan, a province of Pakistan. The survey was designed to assess the level of staffing and facilities in the neonatal health care units. Data were gathered through trained staff either by in-person visits to the facility or via telephone. Results A total of 177 facilities were assessed in 25 districts of Balochistan. A majority (88.7%) of the facilities were from the public sector. Birth and neonatal care services were provided at only 63 (36%) of the assessed facilities and only three had newborn intensive care units (NICUs) with a 1:5 staff: patient ratio. Unfortunately, all NICUs lacked the basic advanced facilities. None of the hospitals had an infection control policy or staff nor any training program for doctors. Conclusion In conclusion, healthcare facilities to manage neonatal patients requiring hospital care are extremely limited in Balochistan and the ones that are available have very limited resources. To improve the healthcare system in Balochistan, all stakeholders should be involved in the planning, decision-making, and implementation of healthcare programs at all levels to ensure sustainability and efficiency.