Apple Valsa canker, caused by the pathogen Valsa mali, is a severe disease which specifically manifests itself on apple twigs and bark but not on leaves, and it affects apple production. In this study, we report the discovery and characterization of a stem-specific cell death-inducing peptide named SDP1, synthesized by an non-ribosomal peptide synthetases (NRPS)-like gene (VM1G_01528), designated as SDG1. The gene is located in secondary metabolite biosynthetic gene cluster 4 on chromosome 2 of V. mali. Deletion of SDG1 significantly impaired the ability of the pathogen to infect apple twigs. Chemically synthesized SDP1 restored the virulence of ΔSDG1 mutant on apple twigs. Moreover, SDP1 induced cell death in apple stem tissue culture, and suppressed the production of lignin, while it had no effect on apple leaves. Single deletions of other genes in the same secondary metabolite biosynthetic gene cluster also abolished the production of SDP1 and reduced virulence on apple twigs. Transcriptome data from apple stem tissue treated with SDP1 suggested that chloroplast activity and auxin responses were inhibited upon SDP1 treatment. Our findings suggest that SDP1 is a novel stem-specific virulence factor that contributes to the virulence of V. mali and may represent a new target for the development of specific disease control strategies.