High mobility group box 1 (HMGB1) is a chromosomal protein in the nucleus and a potent extracellular proinflammatory cytokine, widely described in mammals, nevertheless, with scarce reports in fish. In this study, full open reading frame of HMGB1a gene from Piaractus brachypomus is reported as well as its molecular characterization, including tissue gene expression. At predicted protein level, HMGB1a showed similarities with its orthologs in teleosts and higher vertebrates. The relative gene expression of HMGB1a mRNA was measured in several tissues including the brain, where a differential expression appeared in brain regions, i.e., higher expression in the cerebellum and telencephalon. In addition, in an assay of sublethal exposure to chlorpyrifos, upregulation of HMGB1a was detected in optic chiasm. Furthermore, in a traumatic brain injury model, upregulation of HMGB1a expression was evident 24 hours after lesion and remained higher up to 14 days. These findings suggest a role for HMGB1a in brain damage and its candidature as biomarker of brain injury; however, more studies are required to elucidate the functions of HMGB1a and its regulation in P. brachypomus.