To develop a specific prognostic score for patients with brain metastases (BM) from breast cancer (BC), including the BC molecular subtype and treatment parameters, we analyzed the outcome of 130 patients with BM from BC who received whole-brain radiotherapy. We identified hierarchical risk groups for estimated survival by using recursive partitioning analysis (RPA). Seven prognostic factors, namely performance status, age, trastuzumab-based therapy for HER-2-overexpressing tumors, a triple-negative phenotype, Scarff-Bloom-Richardson grade, the serum LDH level and the lymphocyte count at BM diagnosis, were incorporated in the RPA. The final RPA nodes were grouped according to the survival time. The RPA tree showed that survival was best (median 19.5 months) among patients with HER2-overexpressing tumors who received trastuzumab-based therapy. The worst survival (median 3.5 months) was observed among patients who did not receive trastuzumab and who had lymphopenia at BM diagnosis, or KPS <70 and age over 50 years, or KPS ≥70 and a triple-negative tumor (HR- & HER-2-). The other patients had a median survival of 12.5 months (P < 0.001). This 3-class specific prognostic score successfully predicted the outcomes of a heterogeneous group of patients with brain metastases from BC.