The histopathology of the brain and gill tissues of the fish Cyprinus carpio following exposure to afidopyropen was determined by light microscopy. This particular carp species is one of the most prevalent in India. Afidopyropen (0.2 mg/L) was administered to fish for 1, 10, 20, and 30 days as part of an experiment. The tissues in the control group were found healthy. The abnormalities in the brain were Neural Degeneration (ND) Pyknotic Neuron (PN) Necrotic Internal Granule Cells (NIGC) Demyelination (DM). In gill tissues exposed to afidopyropen, hyperplasia, telangiectasia, epithelial separation, and total destruction of lamellae were seen. In the current study, afidopyropen damaged the organs, indicating its potential for harm. There were no sudden histological changes in one day-exposed group of the fishes. It could be due to healthy fish’s strong and quick adaptation capacity. The severity of stress and the associated histological changes would likely increase over time as the exposure to afidopyropen continues. However, prolonged exposure to the toxicant extremely affects the fish physiology leading to the form of above said pathological lesions.