BACKGROUND: Neonatal mortality remains unacceptably high. Many studies successful at reducing neonatal mortality have failed to realise similar gains at scale. Effective implementation and scale-up of interventions designed to tackle neonatal mortality is a global health priority. Multifaceted programmes targeting the continuum of neonatal care, with sustainability and scalability built into the design, can provide practical insights to solve this challenge. Cambodia has amongst the highest neonatal mortality rates in South-East Asia, with rural areas particularly affected. The primary objective of this study is the design, implementation, and assessment of the Saving Babies' Lives programme, a package of interventions designed to reduce neonatal mortality in rural Cambodia. METHODS: This study is a five-year stepped-wedge cluster-randomised trial conducted in a rural Cambodian province with an estimated annual delivery rate of 6615. The study is designed to implement and evaluate the Saving Babies' Lives programme, which is the intervention. The Saving Babies' Lives programme is an iterative package of neonatal interventions spanning the continuum of care and integrating into the existing health system. The Saving Babies' Lives programme comprises two major components: participatory learning and action with community health workers, and capacity building of primary care facilities involving facility-based mentorship. Standard government service continues in control arms. Data collection covering the whole study area includes surveillance of all pregnancies, verbal and social autopsies, and quality of care surveys. Mixed methods data collection supports iteration of the complex intervention, and facilitates impact, outcome, process and economic evaluation. DISCUSSION: Our study uses a robust study design to evaluate and develop a holistic, innovative, contextually relevant and sustainable programme that can be scaled-up to reduce neonatal mortality. TRIAL REGISTRATION: ClinicalTrials.gov: NCT04663620 . Registered on 11th December 2020, retrospectively registered.