The purpose of this study was to investigate perception of the Food Allergy Labeling System (FALS) of school foodservice in female middle school students. The subjects were 148 female middle school students in the Incheon metropolitan area. In this cross-sectional study, data were collected using self-administered questionnaires. Only 20.9% of subjects had experience of food allergy education. There was no significant difference in food allergy knowledge by grade. The scores of perception of food allergy labeling by school foodservice were significantly higher in lower grade students (p<0.001). In all grades, highest scores were observed for ‘food allergy labeling is necessary’, whereas the lowest scores were for ‘I check the food allergy labeling’. The percentages of subjects who wanted to participate in food allergy education were significantly different (p<0.01); 73.8% in 1st grade, 50.0% in 2nd grade, and 35.7% in 3rd grade. For desired education contents to enhance perception of FALS, 57.5% of subjects answered ‘emergency management’ and 23.0% said ‘information of food allergy causing food’. Therefore, it is necessary to increase food allergy education and educate female middle school students according to grade in order to enhance perception of FALS.