Six-year-old Murtaza is also due to walk out onto the pitch with the Argentinian at Doha's Al-Gharrafa stadium.
Murtaza Ahmadi met the Barcelona forward in Doha, where the Spanish league champions are due to play a friendly match against Saudi Arabian side Al-Ahli later.
Six-year-old Murtaza, from the rural Ghazni province southwest of Kabul, is also due to walk out onto the pitch with the Argentinian at Doha's Al-Gharrafa stadium.
"The image the world wanted to see," tweeted Qatar's 2022 World Cup organisers, who brought the pair together.
"The six year old boy who dreamed of meeting his hero, #Messi, finally comes true."
A delighted Murtaza said: "I'm very happy to have met my hero. It is a dream for me," according to a statement released by Qatar's Supreme Committee for Delivery and Legacy, the committee overseeing organisation of the 2022 tournament.
Murtaza became a worldwide online hit earlier this year after he was pictured wearing his hero's shirt, made out of a plastic bag, with the name Messi and the famous number 10 written on it in marker pen.
The shirt was made by his teenage brother Homayoun after his neighbour threw away grocery bags.
"I love Messi, he plays really well, and I love the shirt my brother made for me," he told AFP at the time.
His family could not afford to buy him a replica kit.
Pictures of Murtaza playing football in his improvised kit were first posted on Facebook.
After the pictures went viral, Murtaza received a real shirt from his hero.
His father, Mohammad Arif Ahmadi, said at the time: "I want my son to become the Messi of Afghanistan."