Bisphenol A, a plastic monomer and plasticizer, is a well-known endocrine disrupter, widely present in the aquatic environment, but little is known regarding its neurotoxicity in fish. Herein, we investigated its effects on male zebrafish brain. Zebrafish were exposed to 10 µg/L BPA for 45 days. An isobaric tags for relative and absolute quantitation approach coupled with nano high-performance liquid chromatography-tandem mass spectrometry analysis was employed to detect and identify differentially expressed proteins. A total of 46 proteins was identified and categorized into functional classes that mostly included metabolism and transport, cytoplasm and organelle, ion and nucleotide binding, indicating that bisphenol A toxicity in fish brain is complex. The biological pathways of starch and sucrose metabolism, calcium signaling, and aminoacyl-tRNA biosynthesis were also induced. Proteomic analyses add new perspectives to bisphenol A neurotoxicity in aquatic organisms.