The pope has been a key supporter of Colombia's peace deal with the Revolutionary Armed Forces of Colombia, or FARC, rebels, even brokering discussions between Santos and his top opposition rival, former president Alvaro Uribe.
"His holiness gave us courage, he gave us momentum, he encouraged all Colombians to persevere in the search for peace and now he will come to Colombia during a unique moment for our country," Santos said after meeting with Colombia's episcopal council of bishops. Francis will visit between Sept 6 and Sept 10.
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Santos won last year's Nobel Peace Prize for his efforts to reach an accord with the FARC, 6,000 of whom are now in the process of handing in their weapons at demobilisation camps.
Francis, an Argentine who also helped broker diplomatic efforts in Cuba and Venezuela, repeatedly expressed support for the deal over four years of often tense negotiations. The visit will be the third by a pope to the Andean nation.
Francis has yet to visit his home country as pontiff.
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