Fault-tolerant lateral waypoint sequencing is provided for a system that includes at least a first flight management computer and a second flight management computer. A processing operation associated with lateral leg sequencing of an aircraft flight plan is implemented in the flight management computers. A determination is made in the first flight management computer as to whether the first flight management computer has received, within a predetermined period of time from when the first flight management computer implemented the processing operation, a notification from the second flight management computer that the second flight has also implemented the processing operation. An action is initiated in the first flight management computer when the first flight management computer has not received the notification from the second flight management computer within the predetermined period of time.