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.
"We will begin proceedings to try to reverse this decision by the Greek court and get his removal suspended," she told AFP.
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.
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Before now, the board had granted asylum to every applicant it dealt with -- all Syrians -- on the basis Turkey was not a safe country for them, according to Pro Asyl. The refugee advocacy group listed 10 such decisions.
A Greek government source dismissed any suggestion the decision was politically motivated, saying each ruling was made on a case-by-case basis.
Greece has been on the front line of an influx of migrants crossing by boat from Turkey as part of Europe's biggest migrant crisis since World War II.
Under the deal struck with Ankara, all Syrian migrants arriving in Greece from March 20 can be sent back to Turkey if they do not apply for asylum or their claim is rejected.
Greece's asylum services have been overwhelmed as many new arrivals have filed applications to try to prevent -- or at least delay -- their return to Turkey.
Thousands of people have been left stranded in cramped detention camps on Greece's islands, known as popular tourist destinations, where violence has boiled over into brawls and arson attacks.
In the latest outbreak, six migrants were injured on Thursday when clashes erupted on the island of Samos, police said, a day after similar violence hit a camp on Lesbos.