Phytochemical analysis of the methanolic extracts of Jatropha podagrica stalks and roots using liquid chromatography-mass spectrometry (LC-MS) led to the isolation of six compounds: corchoionoside C (1), isobiflorin (2), fraxin (3), hovetrichoside C (4), fraxetin (5), and corillagin (6). The isolated compounds (1–6) were tested for their cytotoxicity against MDA-MB-231 human breast cancer cells. Remarkably, compound 4 (hovetrichoside C) exhibited robust cytotoxicity against MDA-MB-231 cells, displaying an IC50 value of 50.26 ± 1.22 μM, along with an apoptotic cell death rate of 24.21 ± 2.08% at 100 μM. Treatment involving compound 4 amplified protein levels of cleaved caspase-8, -9, -3, -7, BH3-interacting domain death agonist (Bid), Bcl-2-associated X protein (Bax), and cleaved poly (ADP-ribose) polymerase (cleaved PARP), while concurrently reducing B-cell lymphoma 2 (Bcl-2) levels. In totality, these findings underscore that hovetrichoside C (4) possesses anti-breast cancer activity that revolves around apoptosis induction via both extrinsic and intrinsic signaling pathways. Display omitted •Phytochemical analysis of Jatropha podagrica led to the isolation of six compounds (1–6).•Among the isolates, hovetrichoside C (4) exhibited robust cytotoxicity against MDA-MB-231 cells.•The cytotoxicity of compound 4 against MDA-MB-231 cells was associated with its ability to initiate apoptotic cell death.•Compound 4 amplified protein levels of cleaved caspase-8, -9, -3, -7, Bid, Bax, and cleaved PARP.•Compound 4 reduced Bcl-2 levels.