Essential oils play pivotal role in sustainably controlling plant pests and diseases. In this study, a synergistic oil-in-water nanoemulsion containing clove (CO) and lemongrass oil (LGO) was developed and explored its potential as antifungal agents against Fusarium oxysporum f.sp. lycopersici (FOL). After initial confirmation of synergism between CO-LGO, a nanoemulsion was formulated using non-ionic surfactants through low-energy emulsification method. The nanoemulsion showed Z-average diameter of 76.73 nm having spherical shaped droplet structure as confirmed by TEM imaging. Minimum inhibitory concentration (MIC) of the optimized nanoemulsion was 4000 mg/l against FOL with the logistic kinetic model demonstrating its notably rapid fungicidal effect. The nanoemulsion disrupted the membrane integrity of FOL as consistently evidenced by sodium dodecyl sulfate polyacrylamide gel electrophoresis, scanning electron and atomic force microscopy. During in planta assay, nanoformulation applied as a soil amendment at MIC reduced the severity of tomato Fusarium wilt incidence up to 70.6% compared with untreated control. The nanoemulsion applied on seedlings and seeds also significantly controlled the wilt disease in tomato without showing any sign of phytotoxicity.