Mr Hollande arrived at the Vatican for the 40-minute private audience on Wednesday after visiting the French church in Rome's historic centre.
He told reporters that he wanted to thank Francis for his solidarity after the Nice attack on July 14 and the subsequent murder of French priest Fr Jacques Hamel in his church in Normandy.
When Pope Francis spoke with Mr Hollande last month, "he told me in confidence that he was standing like a brother by the side of the French people", the French president said.
"All the words that have been said - I'm also thinking of the leaders of the French church - have been very important because they helped remind the French people of their unity... and also of the solidarity of the whole world towards France."
Mr Hollande also pledged to protect French churches and said: "When a priest is attacked, it is all of France that has been hurt."
The Vatican provided no information about the content of Wednesday's audience, but Mr Hollande said he would speak with Pope Francis about refugees, the situation in the Middle East and the plight of Christians who have been targeted in particular by Islamic extremists in Iraq and Syria.
He presented the pontiff with a piece of Sevres porcelain with the French seal on it, the Vatican said.
Pope Francis gave Mr Hollande a bronze sculpture symbolising the passage from war to peace, as well as his recent teaching documents on the environment and families.
It is the second time the two have met privately - Mr Hollande had a state visit on January 24 2014.
