The Iranian construction industry is characterized by chronic schedule delays and cost overruns. While Lean Six Sigma (LSS) has emerged as a hybrid approach to eliminate waste and mitigate errors, its practical implementation is hindered by numerous barriers. This research aimed to identify, structurally analyze, and prioritize the obstacles to LSS implementation within Iranian construction projects. Using a descriptive-quantitative design, challenges were first identified through a literature review, followed by the development of a 42-item researcher-made questionnaire using a five-point Likert scale (ranging from "Never" to "Always"). After content validity was confirmed, the survey was distributed online. Data from 385 completed questionnaires were analyzed. The instrument's reliability was validated with a Cronbach’s alpha of 0.948. Exploratory Factor Analysis (EFA), supported by a KMO of 0.865 and a significant Bartlett’s test (p < 0.001), resulted in the extraction of six factors: Economic and Financial, Executive and Operational, Leadership and Project Management, Human Resources and Supply Chain, Documentation and Scope Changes, and Legal and Contractual challenges. Subsequently, these dimensions and individual items were prioritized using the Friedman test (p < 0.001). Results indicated that Economic and Financial challenges are the highest priority, reflecting the significant impact of macroeconomic conditions on LSS deployment in Iran's construction sector. Based on these findings, strategies such as inflation-resilient financial planning, allocation of contingency reserves, managerial empowerment, and the adoption of digital tools are proposed to enhance LSS implementation.