Non-technical summary Energy sources for the brain include not only blood glucose, but also astrocytic glycogen, especially when the blood-born glucose supply is short (e.g. hypoglycaemia). Although untested, it is hypothesized that during prolonged exercise that induces hypoglycaemia, the resultant hypoglycaemia may cause a decrease in brain glycogen. Here, we tested this hypothesis and provide evidence that brain glycogen decreases during prolonged exercise with hypoglycaemia. Furthermore, in the cortex, we show that the decrease in brain glycogen levels during prolonged exercise is associated with activation of monoamine metabolism, which could be a factor inducing central fatigue. Since the discovery of muscle glycogen depletion as a candidate of peripheral fatigue during prolonged exercise, this is the first study to our knowledge to show that brain glycogen can decrease with prolonged exercise. These findings may provide a clue towards understanding the mechanisms related to central fatigue.Abstract Brain glycogen could be a critical energy source for brain activity when the glucose supply from the blood is inadequate (hypoglycaemia). Although untested, it is hypothesized that during prolonged exhaustive exercise that induces hypoglycaemia and muscular glycogen depletion, the resultant hypoglycaemia may cause a decrease in brain glycogen. Here, we tested this hypothesis and also investigated the possible involvement of brain monoamines with the reduced levels of brain glycogen. For this purpose, we exercised male Wistar rats on a treadmill for different durations (30-120 min) at moderate intensity (20 m min −1 ) and measured their brain glycogen levels using high-power microwave irradiation (10 kW). At the end of 30 and 60 min of running, the brain glycogen levels remained unchanged from resting levels, but liver and muscle glycogen decreased. After 120 min of running, the glycogen levels decreased significantly by ∼37-60% in five discrete brain loci (the cerebellum 60%, cortex 48%, hippocampus 43%, brainstem 37% and hypothalamus 34%) compared to those of the sedentary control. The brain glycogen levels in all five regions after running were positively correlated with the respective blood and brain glucose levels. Further, in the cortex, the levels of methoxyhydroxyphenylglycol (MHPG) and 5-hydroxyindoleacetic acid (5-HIAA), potential involved in degradation of the brain glycogen, increased during prolonged exercise and negatively correlated with the glycogen levels. These results support the hypothesis that brain glycogen could decrease with prolonged exhaustive exercise. Increased monoamines together with hypoglycaemia should be associated with the development of decreased brain glycogen, suggesting a new clue towards the understanding of central fatigue during prolonged exercise.