"I pray to God to support you, so that your country, in keeping with the rich diversity of its moral traditions and its Christian spiritual heritage, continues to seek to build a fairer and more fraternal society," the Argentine pontiff wrote in a telegram.
Relations between the Vatican and the administration of Macron's predecessor Francois Hollande were frosty at times, with the Church having campaigned against the Socialist leader's gay marriage law and then declined to accept an openly gay career diplomat as France's ambassador to the Holy See.
In contrast to Hollande, a self-described atheist, Macron, 39, is of the Catholic faith and was partly educated by Jesuits, the order Francis belongs to.
Under a tradition dating back to the 15th Century, French leaders automatically gain the title of "First and only honorary canon of St John Lateran," the cathedral church of Rome.
And in line with another custom from the time when France had kings, there will be a special mass for the country in St Peter's Basilica on May 30.