The prevalence of overweight and obesity is increasing worldwide, which has been associated with poor cognitive outcomes. Participating in regular physical exercise may also improve cognition, and levels of brain-derived neurotrophic factor (BDNF), but the optimal exercise prescription remains to be elucidated. The purpose of the present study is to compare the effects of moderate intensity continuous training (MICT) and high intensity interval training (HIIT) on cognition, and serum BDNF levels in middle-aged and overweight men. Twenty-five sedentary, overweight men participated in the 8-week training intervention. Subjects were randomized into MICT (n = 12) or HIIT (n = 13) and performed exercise sessions 3x/week for 8-weeks. Cognitive function, and serum BDNF levels were assessed pre- and post-intervention. Statistical analysis was carried out using the Graph Pad Prism 7.0, and the level of significance was set at 5%. Significant improvements were observed in cognitive test scores, and BDNF levels in MICT and HIIT groups (p < 0.05). There were no significant differences in cognitive function between MICT and HIIT. The present study implicates that 8 weeks of MICT or HIIT may be a very useful non-pharmacological treatment option to improve cognitive function, and BDNF levels in middle-aged overweight men.