Rubio is in Italy for a two-day trip aimed at easing ties with Pope Leo after unprecedented attacks on the pontiff by Trump, while also addressing Washington's frustration over Italy's refusal to support the US-Israeli war on Iran.
Meloni had been one of Trump's firmest supporters in Europe, cultivating close ties with him and presenting herself as a natural bridge between Washington and other EU states that had no natural political affinity with the Republican US leader.
But that alignment has come under increasing strain in recent months, as the Iran war has forced her to balance loyalty to the United States against Italian public animosity to the war and the growing economic cost of the conflict.
Before heading to the prime minister's office, Rubio met Italy's Foreign Minister Antonio Tajani, who said the talks had been positive.
"I am convinced that Europe needs America, Italy needs America, but the United States also needs Europe and Italy," Tajani told reporters on Friday.
Meloni and Rubio were expected to discuss the situation in the Gulf, as well as Russia's war on Ukraine, US tariffs on European goods and the outlook for Cuba, which Washington is seeking to isolate both diplomatically and economically.
The Italians will also be keen for a readout on Rubio's meetings at the Vatican.
Trump's recent attacks on Pope Leo crossed a sensitive line in overwhelmingly Catholic Italy and prompted Meloni to call them "unacceptable".
Her criticism in turn drew a sharp rebuke from Trump, who said she lacked courage and had let Washington down.
He subsequently threatened to withdraw US troops from Italy.
Meloni said on Monday she would not support such a move, but acknowledged that the decision "doesn't depend on me".
Italy in April refused to allow US aircraft to use the Sigonella air base in Sicily for combat operations linked to the Iran conflict.
Italian officials have said Washington had not sought prior authorisation from Rome for the use of the site.
Defence Minister Guido Crosetto, a close Meloni ally, later warned that the Iran war was putting US global leadership at risk and said he feared the "madness" of nuclear escalation.
Pollsters say Meloni's ties to Trump could prove a potential liability with voters ahead of national elections due next year.
