Sheona York, the man's solicitor, said the case is believed to be a precedent-setting one in Britain, the Daily Telegraph reported. The Home Office only said it makes asylum decisions on a "case-by-case basis."
Apostasy from Islam is a capital crime in Afghanistan.
"We argued that an atheist should be entitled to protection from persecution on the grounds of their belief in the same way as a religious person is protected," said Claire Splawn, a law student at the University of Kent who helped prepare the case.
A recent court ruling found Scientology is a religion.
The Afghan man, whose name has not been released, became an atheist after his arrival in Britain. In their submissions to the Home Office, York and Splawn said in the interconnected society of Afghanistan it would be difficult for him to hide his beliefs, or lack of beliefs.
They said he visited another Muslim country recently to see friends and was shocked at how different he had become in his attitudes.