Wenzel Wirth, who had travelled with his family to Rome for the day from Verona, ran around the Catholic leader while clergy were reciting teaching in various languages.
Chuckling, Francis said: "And he has something that made me think - he's free. Undisciplined-ly free, but he's free. It made me think, 'am I so free before God?'"
"When Jesus says we have to be like children, it means we need to have the freedom that a child has before his father. I think this child preaches to all of us."
The Vatican gendarmes and the Swiss Guards stood by as the six year darted around the platform, to the amusement of audience members.
When the boy's Argentine-Italian mother tried to fetch her son, she explained to Pope Francis he could not speak.
Ariel Wirth told The Associated Press that Wenzel also experiences behavioural issues and tiredness from a long journey could have prompted Wednesday's episode.
Explaining how the family looks after him at home, Mr Wirth said: "We try to let him be free. He has to express himself, and we live without hiding his problems."
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