Trump has outraged Mexico by vowing to build a wall along the border to keep out migrants, whom he branded rapists and criminals during his presidential campaign.
He has also threatened to put up barriers to Mexican exports, shift jobs from that country back to the United States and even proposed halting remittances by US-based Mexicans back to their families.
Now he has sent Tillerson to Mexico City to smooth over tensions with the country's government.
US officials said Tillerson and Pena Nieto would discuss trade and ways to curb migration and drug trafficking.
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Tillerson will be joined on the trip by US Homeland Security Secretary John Kelly, who was scheduled to travel on to Mexico from an earlier stop in Guatemala.
"It's significant that the president is sending the secretaries to Mexico so early in the administration. It's symbolic of the meaningful relationship that our two nations have," White House spokesman Sean Spicer told reporters in Washington earlier.
Pena Nieto canceled a planned meeting with Trump in Washington last month in reaction to the US leader's vow to make Mexico pay for the wall.