Background: Kisspeptin refers to peptides involved in appetite regulation and responds to energy-decaying agents. The aim of the current study was to survey brain response of kisspeptin and glycogen at different times to acute aerobic exercise with and without glucose solution consumption in male rats. Methods: Eighty adult male Wistar rats, after 2 weeks of familiarization with the laboratory space and treadmill, performed aerobic exercise training for 4 weeks followed by rest for 1 week. Then, based on the weight, they were divided into eight groups: 1, preexercise (PE, n = 10); 2, immediately after exercise (IAE, n = 10); 3, 24 hours after exercise-saline (24HAES, n = 10); 4, 24 hours after exercise-glucose (24HAEG, n = 10); 5, 48 hours after exercise-saline (48HAES, n = 10); 6, 48 hours after exercise-glucose (48HAEG, n = 10); 7, 72 hours after exercise-saline (72HAES, n = 10); 8, 72 hours after exercise-glucose (72HAEG, n = 10). Each exercise session of the rats included running on the treadmill for 90 minutes with a speed of 25 m/min with the slope of zero degrees. Glucose and saline solutions were given to the glucose and saline groups immediately after training. The rats were sacrificed after 3 hours of fasting, and the brain tissue was separated for analysis. Results: No significant difference in brain kisspeptin was seen with time, between groups, and for interaction between time and group (P > 0.05). Tissue glycogen analyses showed significant changes between the groups (P < 0.001). Conclusions: The results of this study showed that brain kisspeptin did not respond to stress and disruption of energy balance and did not relate to the reduction of tissue glycogen in the brain.