Strategic foresight deals with the long term future and is a transdisciplinary exercise which, among other aims, addresses the prioritization of science and other decision making in science and innovation advisory and funding bodies. This article discusses challenges in strategic foresight in relation to transdisciplinarity based on empirical as well as theoretical work in technological domains. By strategic foresight is meant future oriented, participatory consultation of actors and stakeholders, both within and outside a scientific community. It therefore allows multiple stakeholders to negotiate over how to attain a desirable future. This requires creative thinking from the participants, who need to extend their knowledge into the uncertainty of the future. Equally important is skilled facilitating in order to create a space for dialogue and exploration in a contested territory. Although strategic foresight has now been widely accepted for strategy-making and priority-setting in science and innovation policy, the methodologies underpinning it still need further development. Key findings are the identification of challenges, aspects and issues related to management and facilitation of strategic foresight exercises in complex systemic contexts that transcend science in relation to both the persons and problems involved.