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Background Triple negative breast cancer (TNBC) constitutes the most aggressive molecular subtype among breast tumors. Recent studies have shown that autophagy plays a dual role for TNBC. Results We first examined the role of differentially expressed autophagy-related genes in TNBC using high-throughput RNA-seq data from The Cancer Genome Atlas (TCGA). Cox regression analyses showed that EIF4EBP1 and NPAS3 correlated with prognosis in TNBC patients. Multivariate Cox regression analysis showed that expression of these two genes accurately predicted the risk of disease progression in TNBC samples in TCGA and GSE31519 dataset. A nomogram was developed by integrating the risk signature with clinicopathological factor, i.e., TNM stage. ROC curve and calibration plot suggested the nomogram could accurately predict 1-, 2- and 3-year survival rate of TNBC patients. The expression of EIF4EBP1 and NPAS3 also influenced the drug sensitivity of TNBC cell lines. Conclusion In conclusion, the risk signature EIF4EBP1 and NPAS3 as autophagy-related genes could serve as an independent prognostic factor for TNBC patients.