► Review of imaging studies targeting effects of physical activity on cognition. ► Evidence from structural, functional and connectivity data in different age groups. ► Discriminative results for metabolic and coordinative exercise. ► Motor learning research compliments findings of coordination studies. Physical activity has been shown to improve cognitive functioning. Research has largely focused on cognitive facilitation by cardiovascular exercise in older adults. Only few studies have investigated younger age groups or other types of physical activity. In this paper we review and summarize common results found in recent studies of metabolic (i.e. cardiovascular and resistance) and coordinative exercise. Findings from human motor learning are utilized to complement results on coordinative exercise. Results show that both types of exercise affect the brain differently. We propose possible mechanisms by which physical activity facilitates cognitive performance by briefly reviewing microscopic structural changes in animal research. Lastly, we highlight open research questions.