Kirchner traveled to the Paraguayan capital Asuncion on Saturday, accompanied by several high-ranking Argentine officials, the presidency said.
Kirchner will return to Buenos Aires after the mass. Francis is also due to depart Sunday for the Vatican after a trip that took him to Ecuador and Bolivia before Paraguay.
The populist Kirchner and Francis, 78, who has never been afraid to wade into the political arena, were long-time foes and clashed over social issues like same-sex marriage when he was in the Argentine capital.
But the compatriots have made gestures of reconciliation since Francis's election as pope in March 2013.
Francis is the first Jesuit pope and the first pope from Latin America.