The Japanese bunching onion, Allium fistulosum L., is an important vegetable in East Asia. However, the stone leek leafminer, Liriomyza chinensis (Kato), is a serious insect pest that invades the Allium species. As the feeding punctures on the leaf surface caused by the female adults as well as the larval mining inside the unifacial leaves reduce the commercial value of A. fistulosum, it is essential to control L. chinensis during its growth. The accession 'Beicong' has shown resistance to L. chinensis due to its egg-killing defense, but the degree of resistance varies within the 'Beicong' population. Therefore, in the present study, we selected highly resistant selfed lines from the 'Beicong' population by artificially inoculating L. chinensis eggs into the leaves to breed A. fistulosum with a resistance to L. chinensis. A highly resistant line was obtained by continuously self-pollinating the resistant 'Beicong' individual among the 191 individuals, which was inherited in the F-1 hybrid of the resistant line and the susceptible variety. However, the F-1 hybrid's degree of resistance was an intermediate of the two parents'. It was also revealed that the resistance of 'Beicong' was due to both egg- and larval-killing defense mechanisms by artificially inoculating the eggs and larvae into the leaves. Hence, developing a highly resistant line could contribute to integrated pest management in A. fistulosum cultivation by decreasing the population of L. chinensis.