Objectives: The aims of this study were to analyse the expression of CD15s in epithelial (CD44-CD24+) and mesenchymal (CD44+CD24-, CSC) cells in MDA-MB-231 triple-negative breast cancer cell line and to measure expression of CD44 in CSC CD15s+ and CSC CD15s- cells after being treated with thieno[2,3-b]pyridine derivative. Materials and methods: Newly synthesized thieno[2,3-b]pyridine derivative of 3-amino-N-(3-chloro-2-methylphenyl)-5-oxo-5,6,7,8-tetrahydrothieno[2,3-b]quinoline-2-carboxamide was used in 2 μM concentration for 48 hours on MDA-MB-231 cell line. Thereafter, the cells were stained with anti-CD15s secondary antibody conjugated with eFluor 660 on CD15s fluorochrome, anti-CD44-FITC, anti-CD24-PE, and then chromogen fluorescence was analyzed by flow cytometry. Results: There was no difference in expression of CD15s in CSC subpopulation before and after treatment with thieno[2,3-b]pyridine derivative. Unlike CSC subpopulation, this treatment has resulted in almost two times reduction of CD15 expression in CD44- subpopulation (P=0.004). The treatment didn’t have any influence on the expression of CD44 in CD15s+CSC but it had reduced expression of CD44 (P=0.008) in CD15-CSC. Conclusion: The finding of reduced expression of CD15s in epithelial cells and CD44- within mesenchymal cells show the potential of newly synthesized thieno[2,3-b]pyridine derivative as a potential treatment option for triple-negative breast cancer.