Background: Although miR-99b is a known suppressive microRNA in several cancer types, its role in breast cancer is not elucidated. In this study, we examine the clinical relevance of miR-99b expression in breast cancer. Methods: We analyzed microRNA and messenger RNA expressions and their relationships with clinical parameters for 1,961 breast cancer samples from two independent large cohorts, the Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Several algorithms including Gene Set Enrichment Analysis (GSEA) and xCell were used to investigate biological function and the tumor microenvironment. Results: High miR-99b expression significantly enriched the mTORC1 signaling gene set in breast cancer (normalized enrichment score (NES)=1.63, false discovery rate (FDR)=0.03, and NES=1.58, FDR=0.10, in METABRIC and TCGA, respectively). No other mechanisms including the epithelial mesenchymal transition, or nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) and transforming growth factor (TGF)-β signaling, were consistently enriched consistently in both cohorts. miR-99b-high breast cancer was associated with high homologous recombination deficiencies, intratumor heterogeneity, and higher rates of mutation and neoantigens. Further miR-99b-high specimens have increased E2F targets, G2/M checkpoint, and mitotic spindle signaling, and are significantly associated with pathogenesis in both cohorts (p = 0.011, <0.001). High miR-99b was also associated with low stromal cell fractions in the tumor microenvironment, including adipocytes, keratinocytes, and lymphatic endothelial cells (p < 0.001). However, in both cohorts, miR-99b expression was not associated with significant infiltration of immune cells, except for dendritic cells (p = 0.006, 0.020). Finally, in both cohorts, breast cancer with high miR-99b expression was significantly associated with worse and disease-free survival (DSS) and overall survival (OS), particularly in estrogen receptor (ER)-positive/human epidermal growth factor (HER)2-negative breast cancer (DSS hazard ratio (HR) 1.29, 95% confidence interval (CI) 1.10-1.51, p < 0.001 in the METABRIC cohort, and HR 1.82, 95% CI 1.12-2.98, p = 0.017 in the TCGA cohort). Conclusions: Breast cancer with high miR-99b expression was significantly associated with mTORC1 signaling, cell proliferation, and decreased patient survival, particularly in ER-positive/HER2-negative subtype.