Introduction: Patients with distant metastases of borderline phyllodes tumors (PT) are rare, and their prognosis is very poor.Case Presentation: Here, we report the case of a 59-year-old Japanese woman with metastatic brain, lung, stomach, and colon lesions originating from a borderline PT in her left breast. After surgical treatment of the left frontal lobe tumor and the right upper lung tumor, and first-line chemotherapy with doxorubicin monotherapy, magnetic resonance imaging (MRI) revealed new metastatic lesions in the left cerebrum and bilateral frontal lobe. A next-generation sequencing clinical assay revealed that her tumor had platelet-derived growth factor receptor beta (PDGFRB) point mutation (p.N666K). On the basis of genetic analysis, a multitargeted tyrosine kinase inhibitor, pazopanib, was administered as the second-line chemotherapy. Most of her metastatic lesions, including brain metastases, showed a deep shrinkage, which persisted for 12 months.Conclusions: This is the first report that PDGFRB, which is a druggable pathogenic alteration, exists in PT. Genotype-matched therapy can be effectively used to treat rare malignant tumors.