Most Rev Justin Welby praised the renowned physicist, who described himself as an atheist, for a contribution to science which was "as limitless as the universe he devoted his life to understanding".
Dr Ard Louis who attended Cambridge University with Stephen Hawking said he helped believers better understand the complexity of God's creation.
The professor of theoretical physics told Premier: "Professor Hawking did us, as Christians, a favour because he pointed out some of the amazing beauty and intricacy of the world."
According to his family, the British scientist died peacefully at his home in Cambridge in the early hours of Wednesday morning.
Stephen Hawking was initially given only a couple of years to live after he was diagnosed with motor neurone disease in his early 20s.
Responding to the news of Hawking's death, cosmology expert and Christian Dr Rodney Holder expressed hope his views on God changed at the end of his life.
Speaking to Premier, he said: "We are seeing the passing of a great man.
"I hope that perhaps in his dying moments he maybe saw the light that this great universe that he was exploring was actually a creation of a most wonderful God."
Speaking during Prime Minister's Questions in the House of Commons on Wednesday, Theresa May said: "Professor Hawking's exceptional contributions to science and our knowledge of the universe speak for themselves.
"As his children have said, his courage and persistence, with his brilliance and humour, inspired people across the world."
Professor Stephen Hawking was awarded a Nobel prize in 2013, before meeting the Queen in 2014 (pictured).
Click here to listen to Premier's Alex Williams speaking with Dr Ard Louis from the University of Oxford:
Click here to listen to Premier's Alex Williams speaking with cosmology expert Dr Rodney Holder:
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.