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Simple Summary: Breast cancer ranks at the forefront of all malignancies worldwide, and the numerous incidences and mortality rate associated with it are very burdensome to the health care system. Consequently, there is a constant need for new effective drugs with anticancer activity. There have been reports of highly cytotoxic effects of selenium compounds against cancer cells for some time. Hence, our team decided to evaluate the anticancer activity of novel selenoesters in MCF-7 and MDA-MB-231 breast cancer cells. Our results reveal that these compounds are cytotoxic at very low micromolar concentrations, which is associated with the induction of apoptosis and autophagy and arrest of breast cancer cells in the S or G2/M phase of the cell cycle. The obtained results are promising and show that selenium-containing compounds are worth more attention, as they show considerable potential for future candidates as anticancer agents. Disturbing cancer statistics, especially for breast cancer, are becoming a rationale for the development of new anticancer therapies. For the past several years, studies have been proving a greater role of selenium in the chemoprevention of many cancers than previously considered; hence, a trend to develop compounds containing this element as potential agents with anticancer activity has been set for some time. Therefore, our study aimed to evaluate the anticancer activity of novel selenoesters (EDA-71, E-NS-4) in MCF-7 and MDA-MB-231 human breast cancer cells. The assays evaluating proliferation and cell viability, and flow cytometer analysis of apoptosis/autophagy induction, changes in mitochondrial membrane potential, disruption of cell cycle phases, and protein activity of mTOR, NF-κB, cyclin E1/A2, and caspases 3/7, 8, 9, 10 were performed. The obtained results indicate that the tested selenoesters are highly cytotoxic and exhibit antiproliferative activity at low micromolar doses (<5 µM) compared with cisplatin. The most active compound—EDA-71—highly induces apoptosis, which proceeds via both pathways, as evidenced by the activation of all tested caspases. Furthermore, we observed the occurrence of autophagy (↓ mTOR levels) and cell cycle arrest in the S or G2/M phase (↓ cyclin E1, ↑ cyclin A2). [ABSTRACT FROM AUTHOR]