Systems Engineering (SE) allows addressing the design of complex systems from a holistic standpoint, starting from the early stage of development until the end of its lifetime. Using a SE approach, all the stakeholders’ needs can be considered, and different design alternatives can be proposed, taking into account requirements coming from all the different fields connected to component design. Adopting this approach, the ranking of the proposed design alternatives can be carried out using Multi-Criteria Decision Making (MCDM) methods, which foresee the involvement in the decision-making process of a team of experts operating in a participative way. Among MCDM methods, those based on fuzzy logics allow taking into consideration the different shades typical of the experts’ judgement, as the same evaluation might produce different meanings for different people. Fuzzy-based MCDM methods could be advantageous whenever the decision-making process is mainly based on experts’ experience and sensibility, because quantitative data are missing and/or the project is in the very early stage where there is a lack of reliable quantitative information. This is the typical case of R&D activities on nuclear fusion, where big projects (ITER, DEMO) must contend with significant uncertainties. Therefore, a SE approach involving the application of MCDM methods could help to improve the progress of these projects reducing the margins of uncertainty. Several applications are recalled in this paper and a further case study, regarding the Automated Inspection and Maintenance Test Unit (AIM-TU) concept design, is presented. In the framework of  EU DEMO project, the AIM-TU has been proposed to provide to the international community a facility able to perform, with high reliability, robotic maintenance and inspection procedures in DEMO-oriented environments. In this paper the SE approach has been applied to the AIM-TU concept selection, adopting the fuzzy Analytic Hierarchy Process (FAHP) MCDM method for the best option selection. To this purpose,  a novel fuzzy-based decision support tool named ELIGERE has been used. It enables a practical implementation of the FAHP method, speeding up the decision-making process and improving its quality by ensuring the independence of each expert evaluation from the opinion of the other team members.