Trifloxystrobin (TFS) is a widely used strobilurin class fungicide. Ginkgo biloba L. has gained popularity due to its recognized medicinal and antioxidant properties. The aim of this study was to determine whether Ginkgo biloba L. extract (Gbex) has a protective role against TFS-induced phytotoxicity, genotoxicity and oxidative damage in A. cepa. Different groups were formed from Allium cepa L. bulbs subjected to tap water (control), 200 mg/L Gbex (Gbex1), 400 mg/L Gbex (Gbex2), 0.8 g/L TFS solution (TFS), 200 mg/L Gbex + 0.8 g/L TFS (TFS + Gbex1) and 400 mg/L Gbex + 0.8 g/L TFS (TFS + Gbex2), respectively. The phenolic composition of Gbex and alterations in the morphological, physiological, biochemical, genotoxicity and anatomical parameters were evaluated. Rutin, protocatechuic acid, catechin, gallic acid, taxifolin, p-coumaric acid, caffeic acid, epicatechin, syringic acid and quercetin were the most prevalent phenolic substances in Gbex. Rooting percentage, root elongation, weight gain, chlorophyll a and chlorophyll b decreased by approximately 50%, 85%, 77%, 55% and 70%, respectively, as a result of TFS treatment compared to the control. In the TFS group, the mitotic index fell by 28% compared to the control group, but chromosomal abnormalities, micronuclei frequency and tail DNA percentage increased. Fragment, vagrant chromosome, sticky chromosome, uneven chromatin distribution, bridge, vacuole-containing nucleus, reverse polarization and irregular mitosis were the chromosomal abnormalities observed in the TFS group. The levels of proline (2.17-fold) and malondialdehyde (2.71-fold), as well as the activities of catalase (2.75-fold) and superoxide dismutase (2.03-fold) were increased by TFS in comparison to the control. TFS-provoked meristematic disorders were damaged epidermis and cortex cells, flattened cell nucleus and thickened cortex cell wall. Gbex combined with TFS relieved all these TFS-induced stress signs in a dose-dependent manner. This investigation showed that Gbex can play protective role in A. cepa against the phytotoxicity, genotoxicity and oxidative damage caused by TFS. The results demonstrated that Gbex had this antioxidant and antigenotoxic potential owing to its high phenolic content.