This research aims to provide a comprehensive analysis of the impact of applying the Six Sigma methodology on organizational flexibility in the context of the Jordanian Customs Department (JCD). The research seeks to understand the relationship between Six Sigma practices and organizational agility, which is vital for a department to respond effectively to market challenges and organizational changes. The research used a quantitative survey approach to collect data, and data analysis was done using structural equation modeling (SEM) to determine the relationships between variables. The results showed a positive relationship between Six Sigma implementation and JCD flexibility, as adopting Six Sigma practices improved process efficiency and increased organizational flexibility. Based on the findings, recommendations were made including strengthening Six Sigma capabilities, promoting a culture of continuous improvement, and leveraging data analytics to enhance operational effectiveness and responsiveness within JCD. This research contributes to providing empirical evidence on the impact of Six Sigma on organizational resilience in the public sector and provides practical recommendations for organizations seeking to improve their operational performance and adapt in a dynamic and competitive environment.