Maradona, who died on Wednesday at his home in Argentina after a heart attack, met the pope several times at the Vatican after Francis was elected in 2013 as Latin America's first pope.
"The pope was informed about the death of Diego Maradona, he recalls the times he met him in these past years with affection, and he is remembering him in his prayers, as he did in the past days when he was informed about his condition," Vatican spokesman Matteo Bruni said.
Francis is a lifelong fan of the Buenos Aires San Lorenzo soccer team.