The objective of this research is to present a phytochemical profile of Fagonia arabica and to investigate the cytotoxic potential of its extracts against breast, oral, and lung cancer cell lines using MTT assay and dual staining-based mechanistic analysis. The progressive extraction of F. arabica was carried out using the Soxhlet extraction technique. The total phenolic and flavonoid content was calculated as part of the phytochemical profiling performed using GCMS and LCMS methods. The MTT assay was utilized to assess the cytotoxicity against normal L929 cells, as well as malignant A549, MCF-7, and KB-3-1cell lines. The phenolic compounds and flavonoids were the two main elements of the F. arabica methanolic extract, with 1323 µg GAE/g of dry weight and 523.07 µg QE/g of dry weight, respectively. The presence of the functional phytochemicals was verified by GCMS and LCMS analyses. Toxicity testing on the L929 cell line found that the F. arabica methanol extract was the least harmful, with the highest IC₅₀ (296.11 µg/mL). The MTT assay for cell viability against MCF-7 and KB-3-1 yielded significant results, with IC₅₀ values of 135.02 µg/mL and 195.21 µg/mL, respectively. The aqueous extract exhibited significant cytotoxicity against the A549 cell lines (IC₅₀ 116.06 µg/mL). The molecular marker analyses using dual staining revealed that the methanolic extract successfully triggered apoptosis in the different cancer cells tested. The present data suggest that the methanol extract of F. arabica has substantial cytotoxic action against lung, breast, and oral cancer cell lines. Thus, F. Arabica would be a promising source of anticancer medicines, warranting more research to identify the lead molecules with anticancer properties.