Infant Mental Health relates to how well a child develops socially and emotionally from birth to age three. There is a well-established link between parent-infant relationship quality, Infant Mental Health, and longer-term social and emotional development there is a lack of evidence-based interventions that support the parent-infant relationship and/or protect against poor Infant Mental Health. Little Minds Matter is a specialist Infant Mental Health service developed in Bradford (UK) to support parent-infant relationships by providing training and consultation for professionals and direct clinical work to families. The successful implementation of this intervention depends upon how well it becomes embedded within, or integrated into, the early years system. For the purposes of this study, the early years system includes health, social and education services that support child health and development from conception to primary school entry at age five. This study protocol aims to apply a systems approach to evaluate this service and provide a perspective on the process of embedding a complex service within a healthcare system. Multiple methods will be used to investigate embeddedness within the wider early years system. Routinely collected quantitative data about the service will be used to develop a system map showing interaction with related services. Qualitative data will be collected at two time points through interviews with individuals involved in the design and provision of the service, and professionals working within the early years system. Framework analysis will be used to analyse the data inductively and deductively within a systems approach. The findings from this study will provide evidence to inform the ongoing implementation of the service for providers and commissioning bodies. Exploring the application of a systems approach in this clinical context will have application more broadly for researchers evaluating complex interventions and services within a wider system.