The fault modes and system reliability of the flap control system of a certain type of military trainer are studied in the paper. Some possible fault modes of the system are analyzed in detail. The fault tree of the system is built by considering that the flap cannot be laid down. The fault probability of the system and the degrees of importance of elements are computed by means of a new algorithm proposed for network systems in a previous paper. All the results provide a foundation for the maintenance crew in their practical maintenance work.