The 11-year-old boy, Amir, was accompanied by his mother and Greek migration minister Yiannis Mouzalas when he met with Prime Minister Alexis Tsipras, who gave him a Greek flag as a gift.
Amir came to the spotlight last week because while he had been drawn in a lottery to carry the Greek flag in a parade commemorating Greece's World War II struggle, he was ultimately prevented from doing so by his school.
Instead of being given the flag, Amir carried a sign bearing the school's name for the march in Athens.
The ministry of education has launched an investigation into why the school prevented him from carrying the flag.
The annual parades by schools take place around the country on October 28.
"As they haven't given you the Greek flag, I will give you one as a present", Tsipras told Amir, according to the state news agency ANA.
"Some people deprived Amir of the honour to carry our flag. Today I gave it to him so he will remember and honour our principles and values", Tsipras tweeted after the meeting.
Tsipras's symbolic gesture comes after the family's residence in Greece was attacked on Friday.
The assailants broke a window in the room where the family's three children sleep, throwing inside a note warning them to "get out" of Greece.
"It was around three in the morning," Amir's mother told state news agency ANA. "The room was full of glass. The children were scared and were crying. Stones kept coming and a beer bottle was found on the bed."
The family, who have been in Greece for about 18 months, was staying in a flat provided by the city of Athens under a UN-sponsored programme.
Athens mayor Yiorgos Kaminis condemned the incident, insisting that "fascist-style tactics" would not dampen the capital's determination to house and integrate refugees.
Greece is running a programme to house and educate thousands of refugees trapped in the country after a succession of European countries shut their borders last year.
Far-right groups including neo-Nazi party Golden Dawn strongly oppose having the Greek flag carried by non-Greeks in parades.
Golden Dawn supporters disrupted another of the October 28 parades, on the island of Santorini, because the flag was being carried by an Albanian girl.
Eyewitness? Submit your stories now via social or:
Email: eyewitness@pulse.ng
![The 10 warmest years have occurred since 2007 [Black Doctor]](data:image/svg+xml;charset=utf8,%3Csvg%20xmlns%3D'http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg'%20width%3D'300'%20height%3D'172'%20data-ring-placeholder%3D'1'%3E%3C%2Fsvg%3E "The 10 warmest years have occurred since 2007 [Black Doctor]")
