The FET Flagship programme represents a huge investment in strategic and collective research and innovation. It aims at undertaking research and innovation activities that will transform science into technology with significant industrial and societal impacts. The objective is to achieve an effect that is greater than the sum of individual efforts found in national initiatives. Through supporting such work, Flagships will help to successfully position and grow innovative European companies, including SMEs and start-ups, in future global value chains. To evaluate the value of Flagships thus far, a Panel of high-level experts was convened to undertake an interim evaluation of the instrument, and its implementation through the Graphene and Human Brain Projects. The aim was to provide recommendations based on the lessons that can be learned from the implementation and operation of the Flagships. These can then be applied to the implementation of Flagship initiatives that the European Commission may launch in the future.