Allium cepa L. is a well-known traditional medicinal plant with different biological activities distributed worldwide. In the present study, the efficacy of Allium cepa ethanolic extract (EAC) is investigated on biological activity, virulence factors and ERG11 gene expression in C. albicans. EAC was tested against C. albicans growth at the concentrations of 0.125–32 mg/mL. Proteinase and phospholipase activity, cell membrane integrity, hydrophobicity and ergosterol content were determined in EAC-treated and non-treated C. albicans by standard methods. The expression of fungal ERG11gene was studied using Real-Time PCR. The results indicated that EAC strongly inhibited C. albicans growth, reduced proteinase and phospholipase activity, diminished cell membrane integrity, hydrophobicity and affected ergosterol content at the MIC50 concentration. The expression of ERG11gene was suppressed in EAC-treated C. albicans by 47.25%, while it was suppressed by 16.48% for fluconazole-treated fungus in comparison with the non-treated controls. Taken together, the results demonstrated that A. cepa is an effective natural agent capable of inhibiting the growth of C. albicans and suppressing major fungal virulence factors; hence it could be considered as being developed as a phytomedicine in drug discovery against life-threatening candidiasis for therapeutic purposes.