Prior to the boy leaving the hospital, though, medical staff detected he had a fever.
As of Tuesday, Border Patrol agents have started conducting secondary medical checks on all children in CBP custody, including unaccompanied minors and those part of family units traveling with other family members or legal guardians.
The boy was identified as Felipe Alonzo-Gomez, US Rep. Joaquin Castro said. The boy was the second child to die in a US detention center this month.
Alonzo was the second Guatemalan child to die in CBP custody this month after Jakelin Caal, a 7-year-old girl, died December 8.
Here's what we know so far about Felipe's death and the reaction. Migrants from Central America have learned that bringing children to the border makes it extremely unlikely they will be deported and they are taking advantage of that. He was hospitalised twice that day before dying, the agency said.
December 20: They were transferred to El Paso Border Patrol Station. The group of migrants waited eight hours before boarding a bus to the Lordsburg Border Patrol Station.
She'll be in El Paso on Friday and Yuma, Arizona, on Saturday, a DHS official said.
9am: A processing agent at the Alamogordo border patrol station notices Felipe is coughing and has glossy eyes. He is held for continued observation. The child, along with his father, was then taken to a holding facility at a highway checkpoint. They had a hot meal, according to CBP.
10pm: Felipe is nauseous again.
The boy was pronounced dead at 11:48 p.m.
CBP issued a timeline of what it said happened before Felipe's death.
The father, who has not been identified by USA officials, has yet to provide his own version of the events.
Watch the trailer of The Accidental Prime Minister
Presenting the trailer of our highly anticipated film #TheAccidentalPrimeMinister . Gutte, son of Ratnakar Gutte, an MLA from the BJP-allied Rashtriya Samaj Paksha.
US agents say she likely had little to eat and drink before arriving at the USA border, however, her father said that was not true. According to a statement by the Department of Homeland Security, the girl had gone days without food or water.
Felipe and his father were detained by CBP for about a week, an unusually long time that the agency did not fully explain Tuesday.
Felipe González Morales of Chile, who was appointed special rapporteur on the human rights of migrants in June 2017 by the UN Human Rights Council, said American authorities "must ensure that an in-depth, independent investigation" of the girl's death takes place.
Customs and Border Protection Commissioner Kevin K. McAleenan on Wednesday said that his department needs additional help and resources from Congress.
Felipe's father is now being detained at the Alamogordo Station pending transfer to the ICE (Enforcement and Removal Operations).
The deaths have triggered finger-pointing between the White House and Democrats over border security, and allegations that the Trump administration is endangering migrant children by detaining them for days in cells meant as temporary way stations for adults.
CBP released a timeline of the events it says ensued after Felipe and his father, Agustin Gomez, were detained near El Paso on December 18.
DHS wouldn't say exactly how many children are in Border Patrol custody.
So Agustin Gomez grabbed his son Felipe and set out, despite the numerous dangers in such a journey for anyone, much less a child.
But in Felipe's case, the agency hasn't fully addressed why the boy and his father were held in detention for about a week after being apprehended at the border. Numerous claims don't hold up in the end. He also had a fever.
Still, the death of a child in custody is "an extraordinarily rare occurrence", McAleenan told CBS.
Customs and Border Protection revealed that the boy died at a medical center in New Mexico. But officials said they have asked the U.S. Coast Guard, Department of Defense and the Centers for Disease Control and Prevention for help.
Guatemala's Foreign Ministry said the country's government would provide Felipe's father with consular assistance and assume responsibility for repatriating the boy's remains.