Despite research, the role of exercise in treatment and prevention of neurodegenerative diseases remains unclear. Our study, investigated that protective effect of treadmill exercise on molecular pathways and cognitive be-haviours in a scopolamine-induced model of Alzheimer's disease. For that purpose, male Balb/c mice subjected to exercise for 12 weeks. During the last 4 weeks of exercise, mice were given an injection of scopolamine (2 mg/kg). Following injection, open field test and Morris water maze test were used to assess emotional-cognitive behaviour. Hippocampus and prefrontal cortex of mice were isolated, and levels of BDNF, TrkB, and p-GSK3BSer389 were assessed by western blotting, and levels of APP and AB-40 were analysed by immunohistochemistry. In our study, scopolamine administration increased anxiety-like behaviour in open field test, while negatively affecting spatial learning and memory in Morris water maze test. We found that exercise had a protective effect against cognitive and emotional decline. Scopolamine decreased levels of p-GSK3BSer389, BDNF in hippocampus and prefrontal cortex.Whereas TrkB decreased in hippocampus and increased in prefrontal cortex. There was an increase in p-GSK3BSer389, BDNF, TrkB in the hippocampus, and p-GSK3BSer389, BDNF in the prefrontal cortex in the exercise + scopolamine group. Immunohistochemical analysis showed that scopolamine administration increased APP and AB-40 in hippocampus and prefrontal cortex in neuronal and perineuronal areas whereas AB-40 and APP were reduced in exercise + scopolamine groups. In conclusion, long-term exercise may have a protective effect against scopolamine-induced impairments in cognitive-emotional behaviour. It can be suggested that this protective effect is mediated by increased BDNF levels and GSK3BSer389 phosphorylation.