A file transfer system includes a source apparatus and a destination apparatus connected to each other via a predetermined transmission path. The source apparatus includes a source-list generating unit generating a first list, a file storing unit, a list rewriting unit, and a file transmitting unit. The destination apparatus includes a destination-list generating unit generating a second list, a destination-list storing unit, a source-list obtaining unit, a determining unit, a transferred-file storing unit, and a destination-list rewriting unit. The destination apparatus obtains the first list held in the source apparatus, compares the first list with the second list to distinguish an untransferred file from files in the source apparatus, and obtains the untransferred file from the source apparatus while the source apparatus does not rewrite the second list.