This study investigated the antioxidant activity, phenolic content, and cytotoxic effects of Plantago arenaria extracts, alongside the identification of bioactive compounds and their interactions with Crystal structure of human PHGDH in complex with Homoharringtonine (PHGDH). Antioxidant assays revealed significant activity, with a DPPH IC50 value of 266.21 ± 5.44 µg/mL and iron chelating capacity IC50 of 4.22 ± 0.47 mg/mL. The total phenolic and flavonoid contents of the extract were measured at 194.25 ± 34.72 mg GAE/g and 51.47 ± 1.28 mg QE/g, respectively. Phytochemical analysis identified 12 bioactive compounds, with Anisole, o-(1-ethylvinyl)- having the highest percentage at 27.58%. Cytotoxicity studies using SH-SY5Y human neuroblastoma cells showed a 71 ± 2.5% reduction in viability at the highest extract dose, while normal HEK293 cells exhibited significantly increased proliferation, indicating selective cytotoxicity towards cancer cells. Molecular docking studies with PHGDH (7EWH) showed significant binding interactions for several compounds, with 2-Acetylcyclopentanone displaying the highest binding energy of − 4.4 kcal/mol. Toxicity profiling revealed varying degrees of toxicity across different parameters, with Acetic acid, propyl ester, and Anisole, o-(1-ethylvinyl)- being active in cardiotoxicity and carcinogenicity. These findings suggest that P. arenaria extracts possess strong antioxidant properties, significant phenolic and flavonoid content, selective cytotoxicity against cancer cells, and potential for developing PHGDH-targeted cancer therapies.