Managing complex projects is always a challenge. During a project's life cycle, technical, cost, schedule and political complexities can arise. These challenges may include design requirement changes, resource shortages, changes in government regulations, problems with subcontractors, delays in other interdependent projects, which require detailed project plans, particular skill sets, flexibility and constant adaptability. More importantly, organizations need methods to to help managers address complex situations. System Dynamics is a method that can be applied to different areas of knowledge, especially when the system is relatively complex and the behavior of key variables is difficult to predict. This paper describes the use of System Dynamics to help project managers conduct the management process and face uncertainties and complexities. Lessons learned from a Brazilian Air Force Project Management Office – PMO are presented to illustrate insights and key lessons for decision makers.