Chemical-based insecticides/larvicides pose a great threat to humans. The present study describes the histopathological changes in Anopheles stephensi Liston (Diptera: Culicidae) larvae after exposure to two essential oils, i.e. Eucalyptus globulus and Aloe vera. The exposure of 4th instar larvae of An. stephensi to 90 ppm of E. globulus and 550 ppm of A. vera oils resulted in various histological alterations in organs of the head regions like disintegration of the brain and other structures, disorganization in the imaginal buds of the antennae, complete disappearance of the optic lobes, and total disruption of the inner and outer retractor muscles of the brush as compared to the control larvae. Oil-exposed larvae also exhibited diversifications in gastric ceca, disintegration of the midgut epithelium layer, rifts in microvilli, and disappearance or reduction of fat bodies as well as the epithelium layer of the hindgut. Such pathological changes restrict the larvae's ability to perform various functions, leading to their death.