In low and middle-income countries (LMIC) general hospitals are important for delivering some key acute care services. Neonatal care is emblematic of these acute services as averting deaths requires skilled care over many days from multiple professionals with at least basic equipment. However, hospital care is often of poor quality and large-scale change is needed to improve outcomes. In this manuscript we aim to show how we have drawn upon our understanding of contexts of care in Kenyan general hospital NBUs, and on social and behavioural theories that offer potential mechanisms of change in these settings, to develop an initial programme theory guiding a large scale change intervention to improve neonatal care and outcomes.  Our programme theory is an expression of our assumptions about what actions will be both useful and feasible.  It incorporates a recognition of our strengths and limitations as a research-practitioner partnership to influence change. The steps we employ represent the initial programme theory development phase commonly undertaken in many Realist Evaluations. However, unlike many Realist Evaluations that develop initial programme theories focused on pre-existing interventions or programmes, our programme theory informs the design of a new intervention that we plan to execute. Within this paper we articulate briefly how we propose to operationalise this new intervention. Finally, we outline the quantitative and qualitative research activities that we will use to address specific questions related to the delivery and effects of this new intervention, discussing some of the challenges of such study designs. We intend that this research on the intervention will inform future efforts to revise the programme theory and yield transferable learning.