This paper aims to develop a novel methodological approach to evaluation of long-term large-scale research, development, demonstration and deployment (RDDD) programs in energy sector. Following the postulates of “new” endogenous growth theory we propose to amend the evaluation practice with assessment of positive externality effects represented by knowledge, technology and market spillovers. The study examines the case of Controlled Thermonuclear Fusion technology. The appropriateness of different analytical methods for measuring spillover benefits is investigated basing on the documented studies of similar in size and complexity R&D programs, such as CERN, Space exploration program, etc. It is argued that besides the promise of bringing sustainable energy supply in the future, the RD&D and deployment of Fusion technology may yield additional societal benefits which should be taken into account in the allocation of public R&D funds. Paper concludes with practical recommendations how to implement an integrated modelling & assessment framework that could allow for estimating social rate of return of any large-scale energy RDDD program.