In the context of strengthening the fight against doping and limiting the use of synthetic pharmaceuticals, the effective remedies to increase physical performance and accelerate the recovery of athletes are being sought. One of such remedies is exposure to low-level laser radiation (LLLR, LLLT). The study was aimed to investigate the physiological response of highly qualified female rowers’ functional systems to the LLLR irradiation course. To monitor the body of athletes, we used laser Doppler flowmetry (LDF), mathematical analysis of heart rate, neuroenergy mapping, as well as pedagogical testing using the Concept 2 simulator. After irradiation of the neck in the projection of the carotid arteries with pulsed infrared LLLR, the blood perfusion rate increased by 38% (р < 0.05) and cell oxygen utilization rate increased by 48% (р < 0.05). The decrease in the hemoglobin oxygen saturation by 16% (р < 0.05) was also observed. Due to LLLT, the activity of the autonomous regulation mechanism increased with an increase in the total power of the heart rate variability spectrum (TP) by 41% (р < 0.05), and in high-frequency power (HF) by 73% (р < 0.05). The influence of central mechanism decreased with a decrease in amplitude mode (AMo) by 71% (р < 0.05), and in stress-index (SI) by 175% (р < 0.05). Irradiation by LLLR promoted the efficiency of oxygen delivery to certain cerebral cortex areas with the increase of SPL. Аfter LLLT, the speed of 2000 meters distance "passing" by athletes also increased by 3.32% (p > 0.05). The discovered effects of LLLT allow one to expand the range of physiotherapeutic agents that enhance the special physical performance of athletes and accelerate recovery.