Prof Hawking, who had motor neurone disease, died on 14 March, aged 76, at his home in the city.
Up to 500 invited family, friends and colleagues are expected at the private service being held at the university church, Great St Mary's, at 14:00.
Prof Hawking's ashes will be interred next to the grave of Sir Isaac Newton at Westminster Abbey in June.
Although the professor's funeral is private, crowds are expected to gather outside Great St Mary's in the centre of Cambridge to witness the arrival of the funeral cortege on Saturday afternoon.
The funeral will be followed by a private reception at Trinity College.