Lean construction is considered a new methodology for minimizing the causes of waste that hinder the achievement of green building (GB) goals. The main aim of this study is to develop a lean model using fuzzy logic technique to mitigate causes of waste effect in GB projects and to determine the most appropriate lean tools affecting these causes. The inputs of this model include GB waste and four lean tools, comprising Quality Function Deployment (QFD), Last Planner System (LPS), Value Stream Mapping (VSM), and 5S, while the outputs include four improvement level indices based on the lean tools. The model uses various logical rules to achieve several relations among the inputs and outputs, and it is applied and verified using data related to several causes of waste categorized under five groups. The strongest correlation is found between VSM and 5S indices, while an adverse relationship is observed between QFD and 5S indices. The results indicate that a cause of waste that refers to poor assessment of site conditions is considered the most substantial one due to its high improvement level indices across all lean tools. The most significant waste group is related to GB stakeholders, which contains 38% of key causes of waste. The improvement using QFD increases by 10% compared to VSM and 28.20% compared to 5S. QFD and LPS are measured as the most suitable lean tools to mitigate the causes of waste effects due to their high impact and high improvement level indices.