Background/aim: Currently, the equipment and techniques available to assess brain function during dynamic exercise are limited, which has restricted our knowledge of how the brain regulates exercise. This study assessed the brain areas activated during cycling by making use of a novel cycle ergometer, constructed to measure functional MRI (fMRI) brain images during dynamic exercise. Furthermore, we compared brain activation at different levels of ratings of perceived exertion (RPE) generated during the exercise. Methods: Seven healthy adults performed cycling exercise in a novel MRI compatible cycle ergometer while undergoing brain fMRI. Participants completed a cycling block protocol comprising six trials of 2 min cycling with 16-s intervals between trials. Participants reported their RPE every minute through an audio link. The MRI cycling ergometer transferred the torque generated on the ergometer through a cardan system to a cycling ergometer positioned outside the MRI room. For data analysis, the effects of cycling as opposed to rest periods were examined after motion correction. Results: The multiparticipant analysis revealed in particular the activation of the cerebellar vermis and precentral and postcentral gyrus when periods of cycling versus rest were compared. Single participant analysis in four participants revealed that activation of the posterior cingulate gyrus and precuneus occurred in cycling blocks perceived as 'hard' compared with exercise blocks that were less demanding. Conclusions: The present study offers a new approach to assess brain activation during dynamic cycling exercise, and suggests that specific brain areas could be involved in the sensations generating the rating of perceived exertion.