Breast cancer is the most common cancer in women worldwide; despite the developments in diagnosis and therapy, recurrence and metastasis remain the main causes of death among patients with breast cancer. This study aimed to identify a promising biomarker for this disease. The study clarified (1) the association between Friend leukemia virus integration 1 (FLI-1) and various molecular subtypes and (2) the prognostic value of FLI-1 in breast cancer. To the best of our knowledge, this study is the first to report that FLI-1 is a predictor of poor prognosis in patients with breast cancer and overexpressed in the triple negative breast cancer (TNBC) subtype. To further verify the effect of FLI-1 in promoting the metastasis of TNBC, we performed a series of functional experiments in vitro and orthotopic xenograft experiments in the mammary fat pad of nude mice. FLI-1, as a transcription factor, bound to the promoters of key EMT-related genes (CDH1 and VIM), and regulated their expressions at the transcriptional level, thus induced epithelial-mesenchymal transition (EMT). The overexpression of FLI-1 significantly upregulated the expression of mesenchymal markers. After the modulation of FLI-1, the changes in mammary stem cell markers (ALDH1A1 and CD133) and the capacity to form mammospheres were consistent with those of the EMT-related markers. The orthotopic xenograft models further confirmed that the attenuation of stem cell traits after silencing FLI-1 decreased the ability of tumorigenesis. These results indicate that FLI-1 is a useful predictor of poor prognosis in patients with breast cancer. Furthermore, the preliminary exploration of metastatic mechanism in the patients with TNBC will provide a potential target to treat breast cancer in the near future.