Environmental pollution impairs cognitive performance and accelerates its associated age decline. Intranasal (IN) administration constitutes a route for xenobiotics delivery to the brain. The main purpose of the present study was to investigate the long-term consequences of IN administration of a chlorpyrifos formulation (fCPF) (10 mg/kg, every other day, for 15-30 days) in mice. We used a set of behavioral tests and evaluated markers of oxidative stress and the activities of enzymes acetylcholinesterase and glutamate transaminases in different brain areas. After 8 months fCPF-free washout period, fur appearance improved, and the body´s injury number decreased in the fCPF group. Scores in locomotion, recognition memory, and anxiety were similar between control and fCPF-treated mice. Notably, improvements in spatial learning and memory were observed in the fCPF group. Several changes in neurochemical markers of oxidative stress and the activities of enzymes from cholinergic and glutamatergic pathways were observed in different brain areas from fCPF-treated mice. Neurochemical disturbances in the intranasally fCPF group were modeled using the human neuroblastoma cell line SH-SY5Y, treated with fCPF and CPF. Here we show that a previous IN exposure to fCPF induces long-term changes in brain biochemistry. These disturbances, acting in concert, could be responsible for the described behavioral observations. Our results emphasize the importance of the IN pathway on the access of xenobiotics to the brain.