The driver from Southampton in Hampshire reacted with "shock" and "horror" last Sunday when he saw the slogan and walked out of his shift in protest, the BBC reported.
"I was just about to board and there it was staring me in the face, my first reaction was shock horror," driver Ron Heather told BBC radio.
"I felt that I could not drive that bus, I told my managers and they said they haven't got another one and I thought I better go home, so I did," he said.
"I think it was the starkness of this advert which implied there was no God."
The protest comes amid a growing campaign by atheists that started in Britain earlier this month and has spread to Spain, with a similar initiative planned in at least one city in predominantly Catholic Italy.
The slogans have been plastered on 800 buses across Britain and in London's subway system in a move backed by the British Humanist Association (BHA).
The advertisements have been condemned by clergy in Italy and Spain, while angry Christians have protested to Britain's advertising watchdog -- asking for proof that the slogans are telling the truth.
The ads in Britain were the brainchild of comedy writer Ariane Sherine and were financed by more than 140,000 pounds in public donations.
Sherine has said she objected to Christian adverts on some London buses that carried an Internet address warning that people who rejected God would spend eternity in "torment in hell."
Sherine, 28, sought five-pound donations towards a "reassuring" counter-advertisement and won support from the BHA and atheist campaigner Professor Richard Dawkins.
Heather's employer First Bus said it would do everything it could to ensure that he did not have to drive the offending buses. After meetings with First Bus managers on Monday, Heather has agreed to return to work.