The strike is the latest in a series of industrial actions since last year, which have been taking place because of a dispute over new contracts.
The government says the contracts will create a "truly seven-day NHS" with staffing levels the same at weekends than during the week. It has said it has also offered a rise in basic pay.
The British Medical (BMA), which represents doctors, has said the contract cuts anti-social hours pay for nights and weekends, which - even with a rise in basic pay - amounts to an overall pay cut.
Dr Peter Saunders, from the Christian Medical Fellowship, told Premier: "I think prayer is incredibly important.
"The whole situation is a deadlock really since talks broke down. We have a situation where of the 53,000 junior doctors in England, 78 per cent of them are still on strike.
"Primarily we should pray for the BMA and the government to get round the table again and hammer out a compromised agreement that's going to be helpful for people.
"Otherwise, we should be praying that patients would be protected from any harm."
Dr Saunders also said that it is important people aren't pressured into taking one side over another.
He said: "I think it would be fair to say that doctors would feel that the situation currently with the new contract is unjust.
"It's a matter of what action one takes and that's going to be a matter of conscience between each person and the Lord."
Listen to Premier's Antony Bushfield speaking to Dr Peter Saunders speaking:
