Background: The estrogen receptor (ER)-negative/progesterone receptor (PR)-positive (sPR positive) phenotype is an infrequent and independent biological entity. However, the prognosis of patients with sPR positive and her-2 negative phenotype is still controversial, and it is not always easy to decide treatment strategies for them. Methods: Patients during 2010–2014 were identified from Surveillance, Epidemiology, and End Results (SEER) database. The Kaplan-Meier method was used to evaluate cancer-specific survival (CSS). The propensity score matching (PSM) method was used to balance differences of characteristics in groups. The Life-Table method was used to calculate 5-year CSS rates and the annual hazard rate of death (HRD). Results: A total of 97,527 patients were included, and only 745 (0.76%) patients were sPR positive phenotype. The majority of sPR positive breast cancer were basal-like subtype. Survival analysis showed that the sPR positive breast cancer had similar prognosis comparing to ER-negative/PR-negative (dHR negative) breast cancer, and had the highest HRD during the initial 1-2 years of follow-up, then maintained the HRD of almost zero during the late years of follow-up. Conclusions: The patients with sPR positive and her-2 negative breast cancer, similar to dHR negative breast cancer, had a worse survival, and could benefit from chemotherapy significantly. However, the escalating endocrine therapy was not recommended for sPR positive patients. The patients with sPR positive should be excluded from future clinical trials concerning endocrine therapy.