Here, we report a novel comparative assessment of preparation and characterization of thyme oil nanoemulsion and its chitosan encapsulation using high energy approach for the management of three major mosquito species viz., Anopheles stephensi (Liston,1901), Aedes aegypti (Linn., 1762) and Culex tritaeniorhynchus (Giles, 1901). The synthesized formulations were analysed for thermodynamic stability, indicating 1:0.5 (oil: surfactant) ratio to be the most stable of thyme oil nanoemulsion while 1:1 (nanoemulsion: chitosan solution) ratio of its chitosan encapsulation. These were further characterized by dynamic light scattering and transmission electron microscopy which revealed the size and morphology of the droplets which measured 52.18 ± 4.53 nm for thyme oil nanoemulsion and 50.18 ± 2.32 nm for its chitosan encapsulation. All the droplets were well dispersed with distinct flower-shaped nanoemulsion and somewhat mitochondria like chitosan encapsulation. In-vitro release study of thyme essential oil from its nanoemulsion and chitosan encapsulation showed that 91.68% and 73.41% of the total oil concentration in water was released respectively to the environment after 48 h clearly depicting controlled release in the encapsulation. Assessment of insecticidal potential against selected mosquito species revealed that both the nanoemulsion and its chitosan encapsulation were effective on the major mosquito species. Maximum activity of thyme oil nanoemulsion was noticed against C. tritaeniorhynchus (LC -22.58 ppm) after 24 h of exposure while it was observed that its chitosan encapsulation was most effective on A. stephensi (LC -18.88 ppm) after 24 h of exposure. Consistent morphological alterations could be noticed in the larvae of mosquito species. Hence, these nanoemulsions and encapsulations could be further tested for their applications against other insect pests in agriculture.