The purpose of this study was to investigate the fluctuation of the recovery period of autonomic nervous activity (ANA) after isokinetic exercise. Sixteen male subjects participated in this study after they turned in their consent forms. The subjects performed isokinetic knee extension-flexion exercise using BIODEX. We obtained the electro-cardiogram during the entire experiment. We calculated their heart rate (HR) and power spectral of R-R interval (LF is low frequency component, and HF is high frequency component. Both indexes were converted to a logarithm transformation as to lnHF and lnLF.) from pre-exercise period (PRE) and post-exercise period (POST). Some researchers reported that ΔlnHF of POST was lower and ΔLF/HF of POST was higher than those of PRE immediately after aerobic exercise; however, this study's results were in complete contrast. In conclusion, we found that the recovery periods after aerobic and isokinetic exercises of ANA are entirely different.