Lebanon is providing sanctuary to an estimated 1.5 million Syrian refugees, with potential consequences for its health system. Here, we analyse how it has responded to this challenge, identify sensitive areas where a strong national governance system is needed and explore how it might be implemented. An effective response to the Syrian refugee crisis requires concerted international action. Nonetheless, geography dictates that the Lebanese health system must play a central role. We identify some areas where a strengthened stewardship role of the Ministry of Public Health is urgently required. We argue that the Ministry is well placed to take a lead, with its detailed knowledge of the Lebanese health system and its legitimacy to formulate a national health response. Finally, we suggest that this crisis could be a catalyst for the strengthening of the Lebanese health system, based on evidence-informed policies that would benefit refugees and the Lebanese population alike.