Reconstruction project management in the cities of Mosul, Anbar, and Tikrit, in Iraq still faces major obstacles that impede the comprehensive performance of these projects. It is thus necessary to improve the arising challenge estimation in the implementation of reconstruction projects and evaluate their components: time, cost, quality, and scope. This study used the Analytical Hierarchy Process (AHP) to prioritize major and minor criteria in the influential causes of challenges and formulate a mathematical model to help decision-makers estimate them. Using the Super Decisions software, the final results indicated that changes in scope reached 40.8%, which is the greatest difficulty, followed by changes in cost at 27.6%, changes in time at 13.5%, and changes in quality at 18.11%. The results of the essential subcriteria also indicated that underlying issues still exist in the Iraqi construction industry and that quick solutions are vital. Five mathematical equations were formulated to develop a model to estimate changes that introduce challenges in time, cost, quality, and scope and so to help decision-makers assess the level of these changes and identify challenges. This study recommended addressing these variables through realistic administrative and methodological strategies to consider changes, challenges, and available opportunities.