We report the first fatality caused by novel influenza A (H1N1) infection despite having the diagnosis confirmed and being given antiviral treatment after hospitalisation. This patient was also the first with influenza A (H1N1) to be supported with extracorporeal membrane oxygenation in Hong Kong. Although extracorporeal membrane oxygenation is an effective means of supporting patients with refractory hypoxaemia on high mechanical ventilatory support, it is labour-intensive and technically demanding. We also discuss the challenges faced when managing this case.