On August 25 2017, an unprecedented influx of Rohingya refugees began from Rakhine State in Myanmar into Bangladesh's district of Cox's Bazar. The scale and acuteness of this humanitarian crisis was unprecedented and unique globally, requiring strong coordination of a multitude of actors. This paper reflects on the health sector coordination from August 2017 to October 2019, focusing on selected achievements and persisting challenges of the health sector strategic advisory group (HSSAG), and the health sector working groups including epidemiology and case management, sexual and reproductive health, community health, mental health and psychosocial support, and emergency preparedness. In the early days of the response, minimum service standards for primary health care were established, a fundamental initial step which enabled the standardization of services based on critical needs. Similarly, establishing standards for community health outreach was the backbone for capitalizing on this important health workforce. Novel approaches were adopted for infectious disease responses for acute watery diarrhoea and varicella, drawing on inter-sectoral collaborations. Sexual and reproductive health services were prioritized from the initial onset of the crisis and improvements in skilled delivery attendance, gender-based violence services, abortion care and family planning were recorded. Mental health service provision was strengthened through community-based approaches although integration of mental health programmes into primary health care has been limited by availability of specialist psychiatrists. Strong, collaborative and legitimate leadership by the health sector strategic advisory group, drawing on inter-sectoral collaborations and the technical expertise of the different technical working groups, were critical in the response and proved effective, despite the remaining challenges to be addressed. Anticipated reductions in funding as the crisis moves into protracted status threatens the achievements of the health sector in provision of health services to the Rohingya refugees.