Abstract This paper proposes a systematic methodology for supply chain planning optimization and assessment of different scenarios. This methodology will help companies throughout the difficult process of strategic decision-making in what concerns the design of an efficient supply chain structure. The proposed methodology allows the analysis of complex systems as it integrates a decision support tool developed to agile the process of scenario comparison, when designing network structures. This tool allows practitioners to take advantage of the optimization models without the need of learning modelling languages. An example based on a real case study is presented, showing the methodology/tool applicability.