Mercury is a heavy metal responsible for human intoxication worldwide and especially in the Amazon, where both natural and anthropogenic sources are responsible for exposure in riverine populations. Methylmercury is the most toxic specie of mercury with recognized neurotoxicity due to its affinity for the central nervous system. S100B protein is a well-established biomarker of brain damage and it was recently associated with mercury-related neurotoxicity. Accurate measurement is especially challenging in isolated/remote populations due to the difficulty of adequate sample conservation, therefore here we use S100B mRNA levels in blood as a way to assay mercury neurotoxicity. We hypothesized that individuals from chronically exposed populations showing mercury levels above the limit of 10 μg/g in hair would present increased levels of S100B mRNA, likely due to early brain damage. A total of 224 riverine individuals were evaluated for anthropometric data (age, body mass index), self-reported symptoms of mercury intoxication, c-reactive protein in blood, and mercury speciation in hair. Approximately 20% of participants showed mercury levels above the limit, and prevalence for most symptoms was not different between individuals exposed to high or low mercury levels. Rigorous exclusion criteria were applied to avoid confounding factors and S100B mRNA in blood was tested by RT-qPCR. Participants with ≥10 μg/g of mercury had S100B mRNA levels over two times higher than that of individuals with lower exposure. A significant correlation was also detected between mercury content in hair and S100B mRNA levels in blood, supporting the use of the latter as a possible candidate to predict mercury-induced neurotoxicity. This is the first report of an association between S100B mRNA and mercury exposure in humans. The combination of both exposure and intoxication biomarkers could provide additional support for the screening and early identification of high-risk individuals in isolated populations and subsequent referral to specialized centers.