•The evaluation of the antifungal properties of Pelargonium graveolens essential oil against the citrus pathogen Fusarium proliferatum was achieved.•Molecular docking study was carried out to give insights into the interactions of five derivatives with the binding sites of trichodiene synthase from the Fusarium.•The drug-likeness property of the substance was assessed through pharmacokinetic evaluation.•DFT based electronic structure calculations have been carried out at B3LYP/6–31 G (d, p) level of theory. In order to valorize Algerian aromatic and medicinal plants, this study focused on both the evaluation of the antifungal activity of Pelargonium graveolens essential oil against the citrus fungus Fusarium proliferatum and the in-silico study of its fractions. Moreover, the results showed a strong antifungal potential of all tested essential oil (EO) concentrations compared to the commercial fungicide Agriconazole. Five major molecules that, to our knowledge, have not been the subject of any theoretical study are selected to perform the in-silico study. The stability and molecular reactivity of these five molecules were computed using the HOMO-LUMO energies, energy gap, chemical potential (μ), electronegativity (χ), hardness (η), and softness (S) values. In silico analysis through molecular docking and pharmacokinetic evaluation was used to assess its antifungal activity and drug-likeness property. The in silico DFT, ADMET, molecular docking, and molecular dynamics studies confirm that the results have a greater affinity with the in vitro tests carried out for the selection of new antifungal products of natural origin. Display omitted