According to aspects of the embodiments, there is provided an apparatus and method to synchronize trajectories from independent systems such as from a flight management system and the ground Air traffic control during the entire history of a flight. Since a number of trajectory discrepancy factors will intervene during the lifetime of a flight, such as a change in flight intent, controller intervention, or large deviations of the actual flight from the predicted trajectory due to prediction errors, there is need to dynamically monitor these deviations and control a dynamic synchronization cycle. A dynamic trajectory synchronization algorithm attempts to bring each of the systems back into balance whenever a disturbance causes an imbalance. Disturbances include deviation of atmospheric conditions from predicted, change of pilot preference, and unpredicted events requiring controller action, such as need for separation from other aircraft or change in convective weather, special use airspace, or scheduling requirements.