Facility Layout Problem (FLP) is gaining increasing attention among researchers; it is a term relating to the poor layout of facilities as a significant contributing factor of poor performance. FLP is of paramount importance when determining inefficiencies in large room layouts, such as a library building, since the building’s layout closely influences air distribution and impacts on human comfort. Thus, this can lead to unnecessary high energy use to mitigate any inefficiencies. This problem is classified as an NP-hard problem (non-deterministic polynomial-time hardness), considering the various factors influencing thermal factors and layout design. However, previous research shows a lack of consideration of FLP for large rooms. It is identified that various types of constraints are considered in the layout problem literature, and penalty-based constraints are often being prioritised by mere human judgement and intuition. Hence, the accuracy of the objective decision-making is questionable. Therefore, this study proposes a multi-stage methodology to determine the weight of each constraint for FLP by using a multi-criteria decision making (MCDM) method specific to a library building as a case study exemplar. This study’s main focus is to determine penalty based constraints in meta-heuristic approaches for the effective use of FLP. This study concludes by advocating that the proposed methodological approach can be used to identify the most significant constraints in FLP.