Background: Project delays remain a major challenge in the construction industry due to their impact on project performance, revenue recognition, and contractual risks. This issue occurred in PT Ubinkayu Indonesia’s Project PRJ-155 in Surabaya, where actual progress reached only 44.24% compared with the planned 100%, resulting in a 55.76% schedule deviation. Objective: This study aims to identify the root causes of project delays, determine improvement priorities, and develop an integrated Project Control Framework to enhance project performance. Methods: A mixed-method case study was conducted using the Define–Measure–Analyze (DMA) approach from Lean Six Sigma, combined with Lean Construction principles. Quantitative analysis evaluated project performance indicators, including labor productivity, planning reliability, workflow stability, corrective activities, rework rate, and workforce utilization. Qualitative data were collected through observations, interviews, document reviews, and focus group discussions. A Current Reality Tree (CRT) was applied to analyze causal relationships, while the Analytic Hierarchy Process (AHP) was used to prioritize improvement alternatives. Results: The study identified the absence of a structured project control mechanism as the main cause of delays, leading to unstable workflows, shifting priorities, excessive workforce movement, corrective activities, and rework. Three improvement initiatives were proposed: Progress-Based Productivity Management, Installation Readiness Gate with Constraint Heatmap Planning, and Progressive Installation Inspection. AHP results showed that Installation Readiness Gate with Constraint Heatmap Planning was the highest-priority initiative. Conclusion: The proposed framework can improve planning reliability, labor productivity, workflow stability, and project completion efficiency while reducing corrective activities, rework, and financial risks associated with delays.