The disciples believed that God could do miracles — they had cast out demons themselves. But in this case, they weren’t able to see deliverance. I believe the reason the disciples had unbelief was because the epileptic boy fell on the ground, wallowed, and foamed at the mouth (Luke 9:42). It made their senses stand at attention. They said, “It’s not working. This guy is getting worse instead of better.” Their senses dominated them. They had a natural unbelief that stopped them from seeing a miracle. Jesus said to them, “All you need is a little bit of faith, but your unbelief was opposing it.” He said, “You can’t get rid of this kind [in other words, this kind of natural unbelief] except by prayer and fasting.”
Now why does prayer and fasting work? Basically, it works because it brings your senses under control of your spirit and exalts spiritual truth above natural truth.
Your body is not the way you may have pictured it. It is not as strong as you think. Your body literally does what you tell it to do. It is not evil in itself. Likewise, your emotions and senses are not evil in themselves. Satan will tempt them, and if you yield your senses to him, they can become instruments for evil. But your body and your senses in themselves are not evil or good. They’re amoral. They’re natural.
God gave you your body and senses. It’s the way you use them that corrupts you. It’s like a child. A child has certain tendencies to be self-centered, pleasure-seeking, rebellious, etc. Those things in themselves aren’t bad unless you let them become dominant. You’ve got to direct them. You’ve got to channel them in the right direction. Your body, your carnal nature (what the New Testament calls the flesh), is the same way.
So how do you bring it under control? One way is by prayer and fasting.