The purpose of this study was to investigate the effect of transcranial pulsed current stimulation (tPCS) on fatigue delay after medium-intensity training. Materials and Methods: Ninety healthy college athletes were randomly divided into an experimental group (n = 45) and control group (n = 45). The experimental group received medium-intensity training for a week. After each training, the experimental group received true stimulation of tPCS (continuous 15 min 1.5 mA current intensity stimulation). The control group received sham stimulation. The physiological and biochemical indicators of participants were tested before and after the experiment, and finally 30 participants in each group were included for data analysis. Results: In the experimental group, creatine kinase (CK), cortisol (C), time-domain heart rate variability indices root mean square of the successive differences (RMSSD), standard deviation of normal R-R intervals (SDNN), and frequency domain indicator low frequency (LF) all increased slowly after the intervention. Among these, CK, C, and SDNN values were significantly lower than those in the control group (p < 0.05). Testosterone (T), T/C, and heart rate variability frequency domain indicator high frequency (HF) in the experimental group decreased slowly after the intervention, and the HF value was significantly lower than that in the control group (p < 0.05). The changes in all of the indicators in the experimental group were smaller than those in the control group. Conclusion: The application of tPCS after medium-intensity training enhanced the adaptability to training and had a significant effect on the maintenance of physiological state. The application of tPCS can significantly promote the recovery of autonomic nervous system function, enhance the regulation of parasympathetic nerves, and delay the occurrence of fatigue.