The unnamed man fled to the UK from a conflict involving his family in Afghanistan in 2007, aged 16, and was allowed to stay in the UK until 2013.
He was brought up a Muslim, but during his time in the UK became an atheist, the BBC quoted his legal team as saying.
They said he would face persecution and possibly a death sentence if he was returned to Afghanistan.
Lawyer Sheona Yorke, who worked on the case, said that this is believed to be the first case of its type in Britain.
They said the man's return to Afghanistan could result in a death sentence under Sharia law as an apostate - someone who has abandoned their religious faith - unless he remained discreet about his atheist beliefs.
The British Humanist Association said the case may well have a claim to be a first in being based on non-religious beliefs.
"It is great to see Britain showing a lead in defending the human rights of the non-religious in the same way," Chief executive of the association Andrew Copson said.
The Home Office said it did not comment on individual cases.
"The UK has a proud history of granting asylum to those who need it and we consider every application on a case-by- case basis," it said.
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