The boy, identified only as Edgar, was charged with homicide, transporting drugs and possessing weapons illegally, The Associated Press said.
He has already confessed to beheading four people, whose bodies were found hanging from a bridge in Cuernavaca, a tourist hotspot near Mexico City.
If found guilty, Edgar faces three years in prison. The sentence is short because he is charged as a juvenile.
Rumors of a child assassin working on behalf of a drug cartel gripped Mexico last year. Edgar, who was born in San Diego, Calif., was arrested in December as he tried to board a plane from the central Mexican city of Cuernavaca to the border city of Tijuana.
Prosecutors say that Edgar, also known as El Ponchis, worked for Juan "El Negro" Padilla, an alleged local drug kingpin. Authorities say that Padilla is trying to seize control of the drug business in the state of Morelos, to the northwest of Mexico City.
Drug violence killed more than 15,000 people in Mexico last year as drug cartels fight to gain access to the lucrative U.S. market for narcotics such as cocaine and marijuana.
Some claim that the drug lords are recruiting younger and younger boys to serve as foot soldiers.
Edgar's father, David Antonio Jimenez Solis, says his son is not involved in the drug violence. He says that Edgar's confession was made under the threat of violence.
Jimenez Solis has not had any contact with his son since the boy was arrested.
The boy's mother, Yolanda Jimenez Lugo, pleaded guilty last month to charges that she was in the United States illegally.
She's expected to serve a short prison term and then be deported to Mexico, NBC San Diego reported.
Lugo has been estranged from her children since 1996.