When individuals select their own exercise intensity, the factors contributing to the perception of exercise intensity are important. In particular, it is not clear whether the activity of the skeletal muscles influences the self-selected (SS) intensity. Previous investigations have reported that effort sense increases in response to greater neuromotor activity as measured by electromyography (EMG) during dynamic exercise. The purpose of this study was to examine the effects of skeletal muscle activity on SS exercise intensity by investigating the relationship between the ratings of perceived exertion (RPE) and EMG response. Seven healthy men (mean±SD, 22.2±0.4 years) performed two 20-min sessions of cycling exercise with a protocol involving the SS method, which consisted of 5 min of fixed-load cycling at 70% of maximal oxygen uptake followed by 15 min of cycling with the SS method (SSFL_<70%>). RPE in the femoral region (RPE-peripheral: RPEp) was not correlated with the percentage peak wattage (% W_) and EMG indices in the femoral region during the SS protocol. While correlation coefficients between RPEp and EMG indices showed significantly negative values during the SSFL_<70%> protocol, there was no significant correlation between them during the SS protocol. These results during SSFL_<70%> suggested that the decrease of agonist muscle exertion and stress in the joint were caused by the increase in revolutions per minute during cycling. The increase in revolutions per minute during SSFL_<70%> appears to affect the decrease in the exertion of the agonist muscles and the stress in the joint and subsequent decline in RPEp. Since exercise intensity with the SS method is thought to be selected on the basis of cognitive feedback, these results suggest that tension of the skeletal muscle and agonist muscular exertion do not influence the perception of intensity during exercise with the SS method.