Duque and Pompeo will seek to "continue strengthening the bilateral relationship and discuss the crisis provoked by the dictatorship in Venezuela," a statement from the Colombia president's office said Thursday.
The meeting, scheduled for next Wednesday, comes after Duque asked countries "that defend democracy" not to recognize the new government of Venezuelan President Nicolas Maduro, due to be seated on January 10.
The socialist leader, who has overseen Venezuela's descent into the worst economic crisis of its history, will start a second mandate after winning an election earlier this year that was branded a fraud by the US, European Union, opposition groups and the Organization of American States.
Colombia, a strategic ally of the United States, is leading the regional opposition to Venezuela, with which it has extremely frayed diplomatic ties.
The arrival of Russian strategic bombers in Venezuela to participate in military exercises at the start of December sent tensions soaring.
Millions of Venezuelans have fled the economic crisis in their country, many into neighboring Colombia. According to the United Nations, 2.3 million people have left since 2015.
Maduro, who frequently denounces plots against him, insisted this month that the United States was planning to overthrow him with the help of Colombia's right-wing government and Brazil's far-right president-elect Jair Bolsonaro.