Whether you burn fat or carbs is a matter of exercise intensity
Exercise intensity is usually measured with the VO2 max. What is it? VO2 max is a number that determines your body’s ability to consume oxygen. It can be measured in a lab by wearing a mask connected to a machine that estimates your oxygen consumption while running.
The human body consumed mostly fat as a fuel when the intensity level is below 50% of the VO2 max. As the intensity level increases above 50% of the VO2 max, more carbohydrates are burnt as fuel, although fats are used as well. In general, when exercise intensity is between 50 and 70-75%, fats produce 40-50% of the energy (and the rest is produced by burning carbs). At intensity levels above 75%, carbohydrates become the predominant source of energy. This is essentially due to the fact that energy from fats is released slower than energy from carbohydrates, especially at intensity levels above 60% of VO2 max.
Fats come from the adipose tissue, whereas carbohydrates partly derive from blood glucose, although mostly from muscle glycogen. After 90 minutes of continuous training, the contribution of carbohydrates sensibly decreases. At that point, fatty acids become the major source of energy and, since fats are burnt slower, at this stage endurance athletes usually have to reduce their pace and slow down.
It takes 3 hours of exercise at 60-80% VO2 max before glycogen becomes depleted 
Take home messages
- As the intensity level increases, carbohydrates are used as fuel preferably than fats.
- Carbohydrates cannot sustain exercise for more than 90 minutes.
- Prolonged exercise has to be sustained by fatty acids but the pace and the exercise intensity level has to be reduced.
Did you know that?
If you want to lose weight and burn fat, you’d better prefer types of physical activity that will not make you pant too much, since fat is the preferred source of energy at low intensity.
References H. Daries, Nutrition for Sport and Exercise : a Practical Guide. Wiley-Blackwell, 2012.