A gay Syrian whose asylum claim was rejected by Greece will be sent back to Turkey, sources told AFP on Thursday, the first rejected applicant known to be returned under a controversial migrant deal.

The 46-year-old man arrived on the Greek island of Lesbos after the EU struck a deal to send some failed asylum seekers back to Turkey in a bid to stem the bloc's worst ever migrant crisis.

His application was rejected by Greek asylum services and a board of appeal ruled that it was safe to return him to Turkey, said Fotini Barka from NGO the Greek Council for Refugees.

A legal source confirmed the rejection, saying it was the first time such a decision by an appeal board had been made public.

The board heard the Syrian man had already lived several years in Istanbul, Greek news agency ANA reported, where he claimed to have been threatened because of his sexual orientation.