Changes in public health profiles and moves towards inclusive models of education have led to significant number of students in mainstream schools with special health needs. Addressing these needs requires collaboration between health professionals, educators and families. Integrated models of school-based health care can facilitate this collaboration; however, there is little evidence to guide their implementation. The School-Based Primary Health Care Service (SB-PHCS) is one such service that has been established in far west New South Wales. The School-Based Primary Health Care Service embeds health district-employed registered nurses with school learning support teams to increase service access, and improve health and education outcomes for students. We conducted focus groups with nurses and learning support teams to explore their experiences of implementing the School-Based Primary Health Care Service. Focus group transcripts were analysed using framework analysis. We found that defining the role and working across systems were challenges to program implementation, whereas a collaborative culture, relationship building and flexibility in work processes facilitated the integration of nurses into the school teams. We recommend others embarking on similar initiatives involve key stakeholders early in service development, understand each other's systems and processes, and provide clarity about the new role, but plan to adapt the role to fit the context. This study will be of interest to those involved in the implementation of integrated models of school-based health care.