Background: Over the past 20 years, Nepal has seen major improvements in childhood and maternal survival. In 2015, the Nepalese government introduced a new federal political structure. It is unclear how this has affected the health system, and particularly, maternal and child health care. Hence, this study aims to describe and analyse health facility preparedness in the light of the federalization process with regards to providing appropriate and timely maternal and neonatal health services. Methods: A descriptive cross-sectional study was conducted in Jumla district, Nepal in 2019 covering all 31 state health facilities (HF) to assess the availability of maternal and neonatal health services including appropriate workforce and access to essential medicines. Tests of association between demographic factors and the probability of a facility experiencing a shortage of essential medicine within the last 3 months were also conducted as exploratory procedures. Results: Out ot 31 HFs, more than 90% of them had all their staff positions filled. Most facilities (n = 21) had experienced shortages of essential medicines within the past 3 months. The most common out of stock medicine were: Amoxicillin (n = 10); paracetamol (n = 10); Vitamin A (n = 7); and Metronidazole (n = 5). Twenty-two HFs had referred maternal and newborn cases to a higher centre within the past 12 months. However, more worryingly, twenty HFs or their catchment communities did not have emergency ambulance transport for women and newborns. Conclusion: HFs reported better staffing levels than levels of available drugs. HFs should be supported to meet required minimal standards such as availability of essential medicines and the provision of emergency ambulance transport for women and newborns.