Objective: To elucidate the cytotoxic effect of the secondary metabolites of Barrientosiimonas humi (B. humi) on MCF-7 and MDA-MB-231 human breast cancer cells and its underlying mechanisms of action. Methods: The extract was obtained from the fermentation of B. humi and fractionation of the crude extract was conducted via column chromatography. Cytotoxicity of the B. humi extract was determined by using MTT assay and real-time cellular analysis. Morphological changes, cell cycle profiles, mode of cell death, and caspase expressions of control and treated breast cancer cells were determined. Results: The ethyl acetate extract isolated from B. humi was cytotoxic against MCF-7 and MDA-MB-231 cell lines. One of the dichloromethane (DCM) fractions, designated as DCM-F2, exhibited the strongest activity among all the fractions and thereby was selected for further studies. DCM-F2 had selective cytotoxicity on target cells by inducing apoptosis, particularly in the early stage, and cell cycle arrest. Treated cells caused inhibition of cell cycle progression at 72 h leading to a significant increase (P < 0.05) in the G0/G1 population. DCM-F2 treated MDA-MB-231 cells showed caspase-dependent apoptosis, whereas DCM-F2 treated MCF-7 cells showed a caspase-independent apoptosis pathway. Five compounds were successfully isolated from B. humi. Cyclo (Pro-Tyr) was the most cytotoxic and selective compound against MCF-7 cells. Conclusions: B. humi ethyl acetate extract exhibits significant cytotoxicity against MCF-7 and MDA-MB-231 cells via induction of apoptosis and cell cycle arrest.