Exercise at different cadences might serve as potential stimulus for functional adaptations of the brain, because cortical activation is sensitive to frequency of movement. Therefore, we investigated the effects of high (HCT) and low cadence training (LCT) on brain cortical activity during exercise as well as endurance performance. Cyclists were randomly assigned to low and high cadence training. Over the 4-week training period, participants performed 4 h of basic endurance training as well as four additional cadence-specific exercise sessions, 60 min weekly. At baseline and after 4 weeks, participants completed an incremental exercise test with spirometry and exercise at constant load with registration of electroencephalogram (EEG). Compared with LCT, a greater increase of frontal alpha/beta ratio was confirmed in HCT. This was based on a lower level of beta activity during exercise. Both groups showed similar improvements in maximal oxygen consumption and power at the individual anaerobic threshold. Whereas HCT and LCT elicit similar benefits on aerobic performance, cycling at high pedalling frequencies enables participants to perform an exercise bout with less cortical activation.