Border Patrol agents got the information on her movements from two women from India who told officials they'd been separated from a woman and two children traveling in their group hours earlier.
"Agents took the two women into custody and began searching the area north of the international border in remote terrain seven miles west of Quitobaquito Springs," the agency said in a statement. "Within hours, they discovered the little girl's remains."
Agents used helicopters to search for the people she'd been traveling with, and found footprints indicating they returned to Mexico.
"Our sympathies are with this little girl and her family," Tucson Chief Patrol Agent Roy Villareal said. "This is a senseless death driven by cartels who are profiting from putting lives at risk."
CBP said Friday that US Border Patrol agents had located "two missing Indian nationals" after they'd crossed the border back into the United States.
"The mother and her 8-year-old daughter were transported to a local hospital for treatment for dehydration," CBP said.
A decade ago, in 2009, that number was 204.
Update: This story has been updated to give a more precise age for the girl. Pima County Chief Medical Examiner Gregory Hess said she was 6 years and 11 months old.
CNN's Catherine E. Shoichet, Hollie Silverman and Geneva Sands contributed to this report.