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.
While no full road closures are planned, traffic will be held briefly in parts of Cambridge as the funeral cortege passes from the professor's home in the west of the city to King's Parade and the area around Great St Mary's Church.
There is likely to be increased congestion, the university has said.
A condolence book, which was opened on the morning of Prof Hawking's death, will be available to members of the public in the porters' lodge of Gonville and Caius College where he was a fellow for more than 50 years.
A service of thanksgiving for his life will take place at Westminster Abbey in London on 15 June during which time the professor's ashes will be interred next to the grave of Sir Isaac Newton who was buried there in 1727, and close to that of Charles Darwin, who was buried in 1882.
The Dean of Westminster, the Very Reverend Dr John Hall, said it was "entirely fitting" the professor's final resting place should be "near those of distinguished fellow scientists".
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