She said the figure included about 2,500 non-Mexicans, Reuters reported.
Earlier this week, Sheinbaum reached a deal with Trump to pause threatened tariffs on Mexican goods in exchange for deploying thousands of National Guard police to the country's northern border with the United States in a bid to further reduce the flow of US-bound migrants.
Speaking at her regular morning press conference, Sheinbaum added that Mexico has also repatriated deported migrants to Honduras via flights as well as ground transportation.
But she stressed that the repatriations were not forced.
"It's voluntary," she told reporters. "We will accompany them so they can go to their home countries."