(1) Background. Military personel could be defined as “Tactical Athletes”. However, experimental evidence about the effects of new HIIT trainings in comparison with traditional training schedules is lacking. The aim of this study was to experimentally analyze the modifications on psycho-physiological and performance response of soldiers after completing experimental integral operative training. (2) Methods. A total of 43 male subjects of a special unit force of the Spanish armed forces were randomly selected and assigned into the experimental and control groups assessed after training and after deploying in a real operation area. The experimental group underwent an integral operative pre-mission 6-week training (IOT), and the control group, the 6-week traditional training. (3) Results. HIIT-based integral operative training significantly improved combat performance (melee combat score) and the psychophysiological stress response, as measured by heart rate variability indexes. (4) Conclusion. This study provides experimental evidence supporting a new integral operative effective for improved autonomic regulation, reduced perceived stress, melee and close-quarter combat techniques, in addition to aerobic and anaerobic performance and lower body strength in comparison with the traditional training.