Felipe Gómez Alonzo died of Influenza B, complicated by a staph bacteria infection that led to sepsis, the Guatemalan Foreign Ministry said.
Marta Larra, the ministry's spokeswoman, said the Guatemalan authorities received an autopsy report on Monday.
According to the Centers for Disease Control and Prevention, the Influenza B is among the most threatened seasons in the United States.
The New Mexico Office of the Medical Investigator said it has not finalized its autopsy report. Felipe's death, said Alexandra Sanchez, the office's spokeswoman.
The office had said Felipe tested positive for Influenza B but the cause of death was not at the time determined.
CNN has reached out to the US Customs and Border Protection for comment.
The boy died on Christmas Eve at the Gerald Champion Regional Medical Center in Alamogordo, New Mexico, about 90 miles north of the border crossing in El Paso, Texas.
He was detained with his father for an illegal entry Felipe was taken to the hospital after a border agent noticed signs of illness, and the medical staff first diagnosed him with a common cold and ter detected a fever
"CBP said in a statement," The child was held for an additional 90 minutes for observation and then released from the hospital on the afternoon of December 24 with prescriptions for amoxicillin and ibuprofen. " Amoxicillin is a commonly prescribed antibiotic.
The boy began vomiting later that evening and was taken back to the hospital for evaluation. He died hours later, the CBP said.
Felipe's body was repatriated to Guatemala and was laid to rest in Yalambojo in January, his half-sister said.
His father, Agustín Gómez Pérez, was released from CBP custody and is still in the United States, a family member said.
Felipe was the second Guatemalan child to die in the US border patrol custody in December.
Jakelin Caal Maquin, 7, died in a hospital two days after she and her father were taken to a Border Patrol station.
An autopsy report released last week revealed she died from a bacterial infection known as streptococcal sepsis.
The infection was "fast progressive," which led to "multiple organ dysfunction and death," said the report from the medical examiner's office in El Paso County, Texas.
CNN's Nicole Chavez contributed to this report.