The number of babies needing neonatal care is increasing mainly because of technological and therapeutic advances. These advances have implied a decreasing neonatal mortality rate for low birth weight infants and also a falling incidence of preterm stillbirth. Given the structural changes in the National Health Service in England, coupled with recession and capacity constraints, the neonatal system is facing some serious challenges, such as nurse shortages and the lack of cots, which could inevitably impact neonates’ length of stay, and the performance of the system as a whole. These constraints have forced neonatal managers to better understand their organisation and operations in order to optimise their systems. As a result, we have developed three unique methodologies based on length of stay modelling, physical patient pathways, and system dynamics modelling. This paper evaluates these techniques applied to neonatal services in London and showcases their usefulness and implications in practice, particularly focusing on patient flow to determine major drivers of the system, which could reduce inefficiencies, improve patient experience, and reduce cost.