Hawking, a victim of motor neurone disease, died March 14 at the age of 76 at home near the college.
The funeral cortege arrived as the church bell pealed 76 times, one chime for every year of the cosmologist's life.
Hundreds of onlookers applauded outside the church as the hearse containing his remains arrived, according to the BBC.
The famous mathematician's coffin — carried by six porters from the University of Cambridge's Gonville and Caius College — was decorated with white lilies and white roses to represent the universe and the polar star.
The porters were chosen from those who served Hawking in life, assisting the wheelchair-bound professor in public. The author of the amusingly-titled bestseller A Brief History of Time's family honored the helpers by asking them to be pallbearers.
An estimated 500 family, friends and colleagues had been invited to attend a private service inside the church.
On June 15 a service for Hawking will occur at Westminster Abbey in London in which the professor's ashes will be interred adjacent to the grave of Sir Isaac Newton — buried in 1727 — and near Charles Darwin — buried in 1882.
The Dean of Westminster, asserted that it was "entirely fitting" Hawking's remains would reside "near those of distinguished fellow scientists," cited by BBC.