Background Prevention of parent‐to‐child transmission (PPTCT) of HIV is a highly complex package of interventions, which spans services in both maternal and child health programmes. In Papua New Guinea (PNG), a commitment to ensure that all pregnant women and their partners have access to the full range of PPTCT interventions exists; however, efforts to increase access and utilisation of PPTCT remain far from optimal. The aim of this paper is to examine health care worker (HCW) perception of health system factors impacting on the performance of PPTCT programmes. Method Sixteen interviews were undertaken with HCWs involved in the PPTCT programme. Application of the WHO 6 building blocks of a health system was applied, and further thematic analysis was conducted on the data with assistance from the analysis software NVivo. Results Broken equipment, problems with access to medication and supplies, and poorly supported workforce were reported as barriers for implementing a successful PPTCT programme. The absence of central coordination of this complex, multistaged programme was also recognised as a key issue. Conclusion The study findings highlight an important need for investment in appropriately trained and supported HCWs and integration of services at each stage of the PPTCT programme. Lessons from the PPTCT experience in PNG may inform policy discussions and considerations in other similar contexts.