Images of the Prophet are proscribed in Islam. Insulting religion under Pakistan's strict blasphemy laws can carry the death penalty.
The demonstrations were largely led by the Islamist party Tehreek-e-Labbaik Pakistan.
Dozens of men gathered in the northern city of Muzaffarabad in Pakistan-administered Kashmir, yelling slogans that included "Stop barking, French dogs" and "Charlie Hebdo, stop".
"The government of Pakistan should immediately end its diplomatic relations with France as a protest," Sunni cleric Mohammad Zaman said at the rally.
The protest ended peacefully after the men stomped on a French flag, dowsed it in petrol and then set it ablaze.
In a video message, Pakistan's Foreign Minister Shah Mahmood Qureshi said he strongly condemned Charlie Hebdo's action and that he had lodged a protest with the French ambassador in Islamabad.
"The published caricatures have hurt the sentiments of millions of Muslims," he said.
"I hope that this despicable act will not be repeated and those responsible for it will be taken to a court of law."
