The global refugee population has nearly doubled in the last decade, and many of these populations face chronic displacement, often in neighbouring countries with limited resources. Emergency, short-term responses are being transitioned to longer term approaches, including a focus on inclusion through coverage in national health systems. However, analysis of empirical and comparative evidence on how to enact these approaches has been limited. In this article, we analyse the inclusion of refugees in six low and middle-income country (LMIC) health systems (Kenya, Kurdistan Region of Iraq (KRI), Mauritania, Pakistan, Peru and Zambia). Using a shared framework and tools, we collected data over 2023 to 2025, using document reviews, key informant interviews, focus group discussions and participatory workshops. Analysis was carried out separately for each setting, validated locally, and later compared and contrasted for synthesis. We focus on key health system domains – governance, health financing, service delivery (including health workforce) and health information systems - outlining the attributes of refugee inclusion and system integration in each, identifying patterns across the case studies and barriers and enablers. We identify leverage points for improving integration but highlight that inclusion of refugees into national health systems is complex and does not guarantee improved outcomes, especially when refugees previously benefited from a higher level of resources and are being included in strained host health systems. However, committed government leadership, coordinated international support, and multi-year investments in strengthening key components of the local health system, including enabling refugee health staff to engage effectively in it, can make the transition one which benefits both refugee and host communities.