In his column for the BBC Sport website he said: "For the last few days, I have not stopped thinking about Jules Bianchi, after his accident in the Japanese Grand Prix.
"It is so sad he is in such a serious condition in hospital.
"I've literally just been praying like crazy for him - as I'm aware a lot of people have - and I'm hoping for the best."
Bianchi, 25, was unconscious after spinning off the track before crashing into a recovery vehicle.
A CT scan showed he had suffered a severe head injury.
Hamilton has spoken previously about his Christian faith and frequently tweets about going to church.
The 29-year-old also says he prays every day.
Writing in his column, he also remembered another crash that has stuck with him.
He said: "When I was nine years old, I saw a young driver die when I was racing in karts. A good friend of mine who was a good friend of his stopped racing, but that has never been something that has entered my mind.
"That was a very traumatic time for me as a kid. Even now, I can remember standing on the bank beside a track with him with our suits on just before a race, all laughing and joking. And then the next thing I knew I was at his funeral. It was the first time I had ever been to one.
"It is very hard to put that out of my mind at the moment, after what happened to Jules. Things like this really open up your view a bit. Bad things happen to people, but the world keeps going, which is really sad in a way."