BBC reported the Pontiff led the prayers with visitors to his summer residence south of Rome. He expressed sorrow over the deaths caused by the heat.
He also spoke about the environmental damage from the forest fires which have destroyed woodland from Portugal to the Netherlands and Greece.
Forecasters say the high temperatures are unlikely to drop until mid-August.
"I ask you to join me in my prayer for the victims of this calamity and urge all of you to ask the Lord fervently to grant the thirsty Earth the coolness of rain," the Pope said.
He was speaking in Castel Gondolfo, a lakeside town where the weather is generally much cooler for the 83-year-old Pontiff.
Temperatures across the continent have exceeded 104 degrees Fahrenheit (40 Celsius) over the past two weeks. The death toll so far is about 40.