Felipe Gomez Alonso has died of influenza B, complicated by infection with staph bacteria, which has led to sepsis, the Guatemalan Foreign Ministry said.
Martha Lara, a spokeswoman for the ministry, said Guatemalan officials had received a report from the autopsy on Monday.
Influenza B is one of the viruses that cause seasonal epidemics at most winters in the United States, according to the Centers for Disease Control and Prevention.
The New Mexico Medical Investigation Service said she had not finished her autopsy report on Felipe's Death, says Alexandra Sanchez, the spokeswoman for the office.
The office said Felipe had a positive result for influenza B, but the cause of death had not been determined at that time.
CNN reached US Customs and Border Protection.
The boy dies on Christmas Eve at the Gerald Champion Regional Medical Center in Alamogordo, New Mexico, about 90 miles north of the El Paso border crossing point in Texas.
He was detained with his father for illegal entry. about 3 miles west of Passo del Norte entrance in El Paso.
Felipe was taken to the hospital after a border agent noticed signs of illness, and the medical staff first diagnosed him with a simple cold, and Ter detects a fever.
"The child is kept for an additional 90 minutes to watch and then is released from the hospital in the afternoon on December 24 with prescriptions for amoxicillin and ibuprofen," a CBP statement said. Amoxicillin is a commonly prescribed antibiotic
The boy starts vomiting later that night and is returned to the hospital for evaluation. He died a few hours later.
The body Felipe was repatriated to Guatemala and was put to rest in Yalamboho in January, said his half-sister.
His father, Agustin Gomez Perez, is released from the prison of CBP and is still in the United States, said a family member.
Felipe is Guatemala's second child to die in the US Border Patrol in December.
7-year-old Jakelin Kahl Mackin died in hospital two days after she and her father were taken to a border guard station.
An autopsy report published last week is found to have died from a bacterial infection known as streptococcal sepsis. The infection is "rapidly progressive", which has led to "multi-organ dysfunction and death," said the report by the medical expert's office in El Paso County, Texas.
CNN's Nicole Chavez contributed to this report.