Background: This study investigated the anticancer potential of the medicinal herb, Cleome droserifolia (CD), a local plant of the Arabian Peninsula. C. droserifolia is traditionally known for its rubefacient, anti-diabetic, anti-oxidant, and anti-inflammatory properties. Methods: Organic fractions of the aerial parts of Cleome droserifolia harvested from the Arabian Peninsula were tested in human breast and cervical cancer cell lines for their anticancer potential. This was accomplished by using biochemical and cellular assays, including MTT, caspase Glo, western blot, and annexin V/propidium iodide-based flow cytometry analyses. Results: Test of the dichloromethane fraction of the methanolic extract of C. droserifolia, (CDD) revealed potent cytotoxic activity (from 70 to 90%) against several human cancer cell lines, including MCF-7, MDA-MB-231, and HeLa. Further characterization of the CDD fraction in MCF-7 cells revealed that it could activate the enzymatic activity of various caspases in a statistically significant manner, and induce cleavage of both caspase 7 and poly ADB ribose polymerase (PARP) proteins, but not the ethyl acetate fraction. Test of the ability of CDD to induce early signs of apoptosis was validated by annexin V/propidium iodide assay using FACS analysis. Induction of apoptosis was completely reversed by the classic pan inhibitor of apoptosis, Z-VAD-FMK, reducing early apoptosis from 29.7 to 0.6%, confirming that CDD could induce caspase-dependent apoptosis. Conclusions: Altogether, our results reveal that C. droserifolia is a valuable medicinal plant with bioactive molecules that can induce apoptosis in human cancer cells. Thus, this plant should be explored further for its potential as an anticancer natural therapy as well as the isolation of novel molecules with anticancer properties.