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Abstract Background Breast cancer is the most commonly detected cancer and one of the leading causes of cancer mortality. Emerging evidence supports that aberrant expression of lncRNAs is correlated with tumor progression and various aspects of tumor development. Aim This study aimed to evaluate the expression pattern of LINC01116 in breast cancer tissues and investigate the impact of LINC01116 on patients' survival. Methods and Results Microarray and qRT‐PCR data analysis were performed, and the KM‐plotter database was used in this study. In addition, the gain of function approach was performed to examine the effect of LINC01116 on breast cancer cells in‐vitro. The results exhibited that LINC01116 is meaningfully upregulated in the ER+ tumor specimens compared to the ER– ones. Also, relative to normal tissues, the expression of LINC01116 in ER+ and ER– tumor tissues significantly increased and decreased, respectively. ROC curve analysis revealed the power of LINC01116 in distinguishing ER+ from ER– samples. Additionally, the Kaplan‐Meier survival analysis showed that the LINC01116 expression positively correlates with survival probability in all as well as ER+ patients. However, this correlation was negative in ER– patients. Furthermore, our results showed that the overexpression of LINC01116 induces TGF‐β signaling in ER– cells (MDA‐MB‐231), and microarray data analysis revealed that LINC01116 is significantly upregulated in 17β‐Estradiol treated MCF7 cells. Conclusion In conclusion, our results suggest that LINC01116 can be a potential biomarker in distinguishing ER+ and ER– tissues and has different effects on patients' survival based on ER status by affecting TGF‐β and ER signaling.