Introduction: Mental impairments, including deterioration of mood and cognitive performance, are known to occur during isolation and space missions, but have been insufficiently investigated. Appropriate countermeasures are required, such as exercise, which is known to prevent mood disorders for prolonged space and isolation missions. Based on the interaction of brain activity, mood and cognitive performance, this study aims to investigate the effect of long-term isolation and confinement and the long-term effect of exercise on these parameters. Methods Eight male volunteers were isolated and confined for about eight month during the winter period at the Antarctic Concordia Station. Every six weeks electroencephalographic measurements were recorded under rest conditions, and cognitive tests and a mood questionnaire were executed. Based individual training logs, subjects were afterwards separated into an active (> 2500 arbitrary training units/interval) or inactive (< 2500 arbitrary training units/interval) group. Results: A long-term effect of exercise was observed for brain activity and mood. Regularly active people showed a decreased brain activity (alpha and beta) in the course of isolation, and steady mood. Inactive people instead first increased and than remained at high brain activity accompanied with a deterioration of mood. No effect of exercise and isolation was found for cognitive performance. Conclusion: The findings point out the positive effect of regularly performed voluntary exercise, supporting subjective mental well-being of long-term isolated people. The choice to be regularly active seems to support mental health, which is not only of interest for future isolation and space missions.