Aircraft development process is characterized by high complexity and ever-decreasing lead times throughout for shortening time-to-market as an outcome. Development delays experienced in systems integration and the occurrence of design oscillations represent the main threats for the aeronautical industry to accomplish the certifying boards schedules. Planning activities in this dynamic scenario is a very difficult task. This work describes a method based on Petri Nets theory for modeling the problem of flight tests process management for the aircraft certification. The designed planning tool has been used in a demonstration environment that represents the basic problems of a real certification flight test program as a case study. Comparing the conditions with and without the tool, it is possible to conclude that the risk of severe mistakes caused by faulty assumptions for time, cost value and safety can be reduced significantly, since a great number of “what if” scenarios can be checked.