Circular RNAs (circRNAs) are a new class of non-endogenous coding RNA and an area with a lot of research interest and activity. Cypermethrin and chlorpyrifos have been shown to cause serious toxicological damage in the brain of fish and other non-target organisms. However, circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study, circRNAs were identified and characterized using RNA-seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10,375 circRNAs were detected. It was determined that 6 circRNAs were up-regulated, 10 circRNAs were down-regulated in CYP brain samples compared to controls. In addition, it was found that 57 circRNAs are up-regulated and 3 circRNAs down-regulated in CPF brain samples compared to controls. Moreover, 62 circRNAs were down-regulated in the CYP samples, when CYP and CPF samples were compared. However, up-regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway, endocytosis mechanism, apoptosis, and p53 signaling pathway. This study, which was conducted for the first time in terms of the subject of the study, could bring a different perspective, especially to pesticide toxicity studies.