Pope Benedict XVI told President George Abela he hoped to see him next year after the latter invited him to visit for the 1,950th anniversary of St Paul's shipwreck.
President Abela met the Pope at the Vatican City on his first official visit since he took office two months ago.
His first words on leaving the private audience were "it was a profound spiritual experience".
On greeting the President at the Apostolic Palace, the Pope described Malta as a great friend of the Holy See.
The audience lasted about half-an-hour and the subjects discussed included immigration. The President told the press after the meeting that the Pope was well aware of the problems Malta was facing and said the problem had to be address by all countries by helping Africa.
The President invited the Pope to visit Malta next year on the 1,950th anniversary of St Paul's shipwreck. The Pope hinted he would consider the invitation by looking the President in the eye later and saying "I hope to see you next year".
Following the audience, the President met Cardinal Tarcisio Bertone, the secretary of state of the Holy See and tonight he is due to be hosted at an official dinner by Fra’ Matthew Festing, Grandmaster and Prince of the Sovereign Military Order of Malta.
Dr Abela, who is accompanied by Mrs Abela and Foreign Minister Tonio Borg, returns to Malta tomorrow.