Guzman's lawyers say they will appeal against the decision, meaning the process could drag on for months.
The notorious drug lord was recaptured in January, six months after escaping through a tunnel from his maximum-security prison cell.
Mexican authorities transferred him in May to a prison near the US border.
But they denied the move to Ciudad Juarez, just across the border from El Paso, Texas, was a precursor to extradition.Guzman faces charges from seven US federal prosecutors. He is also accused of money-laundering, and arms and drugs possession.
His lawyer, Juan Pablo Badillo, told Reuters news agency he would file "many" legal challenges in the coming days.
Mexico's foreign ministry says the US has guaranteed Guzman will not face the death penalty if the extradition goes ahead.
Born to a farming family, Guzman went on to become head of the Sinaloa cartel, at one point thought to be responsible for a quarter of all drugs entering the US via Mexico.
Before his escape last year Guzman had already fled prison, going on the run for more than a decade.
