Ibrahim al-Hussein crossed the Aegean from Turkey to Greece on a rubber boat in 2014 after having lost part of his leg in a bombing in Syria, the Hellenic Olympic Committee and the United Nations refugee agency (UNHCR) said.
He has since been given asylum in Greece, the main route into Europe from 2015 for more than a million people from conflict-wracked or poor countries in the Middle East, Asia and Africa.
Holding the Olympic flame will be "an honour", the 27-year-old al-Hussein was quoted as saying by the UNHCR website Tracks.
"I am carrying the flame for myself but also for Syrians, for refugees everywhere, for Greece, for sport, for my swimming and basketball teams," said al-Hussein who works in an Athens cafe and trains several times a week.
Up to 10 refugees are to compete in Rio in August under the Team of Refugee Olympics Athletes (ROA), the International Olympic Committee (IOC) has said.
They will be chosen from a pool of 43 prospective Olympians identified by the IOC and supported with funds to train.
The son of a swimming coach, al-Hussein and many of his 13 siblings swam competitively from the age of five. He used a 36-metre high suspension bridge in the city of Deir ez-Zor as a diving board until it was destroyed in 2013 during the war.
His right leg was amputated from the middle of the calf and he walks with a prosthetic leg that a private doctor arranged for him to receive for free.
Al-Hussein trains at a 2004 Athens Olympics complex and also plays for a wheelchair basketball team that travels across Greece for games.
"My goal is to never give up but to go on, to always go forward, and that I can achieve through sport," he said.
The Olympic torch was lit in Ancient Olympia in southern Greece on Thursday, starting a six-day relay across the country.
It will pass through the town of Marathon, which gave its name to the endurance race, as well as the ancient Acropolis.
The torch arrives in Brazil on May 3 for a 100-day relay across that country, featuring around 12,000 torch-bearers, ahead of the Aug. 5 opening ceremony for the first Olympics to be held in South America.
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