Cypermethrin (Cyp), a known neurotoxic pesticide, is widely used in agricultural applications. In the present study, the aim was to determine the histopathological effects of Cyp toxication and evaluate the activation of inducible nitric oxide synthetase (iNOS) and 8-hydroxy-2-deoxyguanosine (8-OHdG) using an immunofluorescence assay. Thereafter, we identified the expressions of caspase 3, capsase 8, iNOS, and metallothionein 1 (MT1) genes in common carp using quantitative reverse transcription polymerase chain reaction (qRT-PCR). High and low doses of Cyp were administered to experimental groups for 24, 48, 72, and 96 h. As a result, necrotic neurons in different stages and desquamation of ependymal cells due to necrosis were detected in the brain. Histopathological changes, including hyperplasia of lamellar cells, telangiectasia of lamellae and thickening due to cellular infiltration in gills, hemorrhage, diffuse hydropic degeneration, and focal necrosis in the liver were observed in the experimental groups. Immunopositive reactions of 8-OHdG were clearly observed in the nuclei and cytoplasm of neurons, and positive reactions for iNOS were detected in the cytoplasm of neurons and in the glial cells of the experimental groups. Furthermore, we found that caspase 3, capsase 8, iNOS, and MT1 genes were up-regulated in the brain when exposed to both high and low doses of Cyp. In conclusion, our findings revealed that Cyp toxication harms the organs of common carp, particularly the brain, and also gives rise to inflammation, DNA damage, and apoptosis. Therefore, the use of Cyp should be restricted to protect the health of aquatic animals.