Dibromoacetic acid (DBA) is a by-product of disinfection in drinking water, which could cause many adverse effects in test animals. However, little research on its neurotoxicity has been conducted, and its mechanism has not been elucidated. In the present study, ninety Sprague−Dawley rats were administered DBA at doses of 0, 30, and 90 mg/kg body weight for 28 days via oral gavage. We found that DBA could induce obvious neurotoxicity in the pineal gland as indicated by histological changes and impaired rhythm of melatonin in pineal and serum. In the mechanism study, transcriptome data showed that DBA exposure could induce 732 differential expression genes. Besides, GO and KEGG analysis results indicated that these genes were enriched in circadian rhythms, among which CREB1 had the most significant fold change. And immunofluorescence staining (IF) and immunohistochemical staining (IHC) results showed that the number of amber-colored masculine neurons for the p-CREB1 in the 90 mg/kg group was markedly lower, and staining for the p-CREB1 was weaker. Moreover, the results of PCR and western blot showed that DBA exposure could down-regulate the expressions of CREB1 and p-CREB1, leading to the decreased expressions of gene and protein of arylalkylamine N-acetyltransferase (AANAT), and then resulting in the impaired melatonin synthesis in the pineal and serum. In conclusion, DBA exposure is associated with abnormal melatonin rhythm via inhibition of the p-CREB1-AANAT signalling pathway.