Fungi, including Rhizoctonia solani and Sclerotium rolfsii, pose a significant threat to agricultural productivity, causing substantial crop yield and quality losses. The excessive use of conventional fungicides raises concerns regarding their environmental impact and human health. This study explores the antifungal potential of thyme and clove oil nanoemulsions as a sustainable alternative. Nanoemulsions were prepared using high-energy ultrasonication and exhibited remarkable stability, with homogenous particle size distributions and low polydispersity index values.  In vitro assays demonstrated complete fungal growth inhibition at 3000 ppm for both oils. Pot bioassays revealed significant antifungal activity, with thyme oil nanoemulsion reducing R. solani and S. rolfsii root rot by 75% and 50%, respectively. Clove oil nanoemulsion also effectively suppressed these pathogens by 41.67% and 25%, respectively. Thyme and clove oil nanoemulsions treatments significantly stimulated root growth under fungal challenge. In this regard, plants treated with thyme oil nanoemulsion showed remarkable increases in root length (4.61-fold and 11.18-fold), fresh weight (28.59-fold and 45.62-fold), and dry weight (48.29 and 48.43-fold) when exposed to R. solani and S. rolfsii infection, respectively, compared to untreated control. Clove oil nanoemulsion also significantly enhanced these root attributes, with remarkable increases in length (1.87-fold for R. solani and 4.12-fold for S. rolfsii), fresh weight (11.09-fold for R. solani and 21.31-fold for S. rolfsii), and dry weight (25.14-fold for R. solani and 16-fold for S. rolfsii). Molecular modeling studies supported the observed antifungal efficacy. In conclusion, thyme and clove essential oil nanoemulsions are promising candidates that act as natural fungicides for managing root rot diseases.