The criminal complaint was made public after Pope Francis said on Monday he would show zero tolerance for anyone in the Church who abused children and compared sexual abuse of children by priests to a "satanic Mass."
The complaint was made last week in the central state of San Luis Potosi against Eduardo Cordova, a priest accused of abusing a 16-year-old boy, said Armando Martinez, president of Mexico's school of Catholic lawyers.
If tried and convicted, the priest could face jail in a major departure from the Church's long-held practice of dealing with such cases in-house.
"It is the first time ... that a priest has been denounced criminally in Mexico," Martinez told Reuters in a telephone interview. "It is not something that fills us with pride, it is simply that we want justice to be done."
Mexico is home to the world's second-largest Catholic community after Brazil.
The Archdiocese of San Luis Potosi said on Tuesday the Vatican had ordered Cordova's removal.
In February, the United Nations Committee on the Rights of the Child accused the Vatican of systematically turning a blind eye to decades of abuse and attempting to cover up sex crimes. The Vatican called the report unfair and ideologically slanted.
A Mexican child abuse victims' support group, the Citizens' Initiative Association, says it has received complaints that dozens of other youths were abused by the priest over several years, and that the Church had been informed in the past.
Cordova also worked as a teacher at a Catholic school.
"The Archdiocese of San Luis Potosi has offered to cooperate with the state attorney general's office to shed light on the crime Cordova is accused of," a spokesman for the attorney general's office said.
The spokesman said he did not know if Cordova would be asked to testify or whether he would be detained.