In construction projects delays are not only disruptive but also expensive. Thus, the reasons for schedule deviation need to be identified. In previous research delay factors were determined predominantly through surveys. In these studies, the reasons for schedule deviation were identified through the point of view of the stakeholders in construction projects. In addition, delay factors are typically considered individually and are presented at the same level. In reality, owing to the complex structure of construction projects and long execution time, non-conformance in schedules occurs by a chain of events. The aim of this research is to investigate the factors causing schedule deviation in construction projects and understand the cause-effect relationships between the events leading to delays. Fault tree analysis (FTA) is an established tool to root cause problems. FTA looks deeply into the chain of events leading to a problem to identify its primary cause. FTA was applied to a modular construction project that experienced significant delays. The analysis identified multiple delay factors, and showed how they are linked from the primary causes to the ultimate event. A comparison was performed between FTA and the conventional deduction method from log books employed by construction companies.