Filariasis is a mosquito-borne disease that causes lymphedema and the main vector is Culex quinquefasciatus. A simple measure was taken to eradicate the vector using nanoemulsion. Eucalyptus oil nanoemulsion was formulated in various ratios comprising of eucalyptus oil, tween 80 and water by ultrasonication. The stability of nanoemulsion was observed over a period of time and 1:2 ratios of eucalyptus oil (6%) and surfactant (12%) was found to be stable. The formulated eucalyptus oil nanoemulsion was characterized by transmission electron microscopy and dynamic light scattering. The nanoemulsion droplets were found to have a Z-average diameter of 9.4 nm and were spherical in shape. The larvicidal activity of eucalyptus oil nanoemulsion and bulk emulsion was tested and compared. Our nanoemulsion showed higher activity when compared to bulk emulsion. The histopathology of larvae-treated and untreated nanoemulsion was analyzed. Furthermore, biochemical assays were carried out to examine the effect of nanoemulsion on biochemical characteristics of larvae. The treated larval homogenate showed decrease in total protein content and a significant reduction in the levels of acetylcholinesterase. The levels of acid and alkaline phosphatase also showed reduction as compared to control larval homogenate.