Speaking after Mrs May was announced as the successor to David Cameron, Rt Revd Richard Chartres said the country was not "facing a Pagan prime minister".
Theresa May, 59, has "profound Christian convictions, not only inherited but also of her own", he said.
Mrs May's father was a vicar in Eastbourne, East Sussex.
She promised to give British people "more control over their lives", after a day of drama in Westminster saw her coronation as David Cameron's successor as Prime Minister.
The Home Secretary will take up office as Britain's second female PM on Wednesday, after Mr Cameron answers MPs' questions in the House of Commons for the last time and goes to Buckingham Palace to offer his resignation to the Queen.
Mrs May was unexpectedly transformed from leadership candidate to prime minister-designate by the sensational decision of her only rival, Andrea Leadsom, to pull out of the race to succeed Mr Cameron, which had been due to last until September 9.
Bishop Richard exclusively told Premier: "We pray for her because we are bound to pray, we pray for her in a situation of great tension and difficulty where it's hard to see how one can find a way forward which is going to achieve majority support.
"We need some calm and judicious leadership at the moment and we must be praying for Mrs May that she'll be given the strength and the wisdom to continue on a course which is bound to be very turbulent and very difficult."
Bishop Richard Chartres speaking exclusively to Premier's Political Editor Martyn Eden: