A statement from CBP says the boy was apprehended and processed by border agents after illegally crossing the border about a week ago near Hidalgo, Texas.
When Customs and Border Protection personnel went to check on him Monday morning he was found unresponsive, and was not able to be revived, a CBP official said.
The cause of death is unknown.
"The men and women of US Customs and Border Protection are saddened by the tragic loss of this young man and our condolences are with his family", said Acting CBP Commissioner John Sanders.
The CBP official briefing reporters Monday said they are dependent on the Health Department to find the space to take the children, and that didn't happen until Sunday.
Four of them died in U.S. custody, while a fifth child, who crossed the border with his mother in April, died this month after weeks in the hospital, but had already been released from custody.
A Border Patrol agent in Arizona sent texts calling immigrants "savages" and "subhuman" the month before using his patrol vehicle to knock over a Guatemalan man who was trying to flee, prosecutors say. "We see this callous disregard for brown, Spanish-speaking children". The official said CBP facilities have medical providers who can monitor detainees, though the official did not know what specific symptoms Carlos had.
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Bowen was among three agents who approached the man, since identified as Guatemalan national Antolin Lopez Aguilar, 23, after spotting him hiding under a semi-trailer.
When he was hit the first time, the man "reached back while running and used his hands to "push off" of the hood" according to an affidavit filed by the Department of Homeland Security's Office of Inspector General.
However, the deaths also come as migrant family units and unaccompanied alien children (UACs) are descending on the southern border in record numbers. From October 2018 through this April, almost 293,000 unaccompanied children or people travelling in families were apprehended at the southern USA border - almost four times the number during the same period the prior year.
"We asked them where they were going to drop us off and they said at a bus station and there you might find some people who can help you, and that's it", said Angel Gonzalez, 34, who left Guatemala on April 25 with his 11-year-old son and traveled through Mexico before crossing the USA border.
On April 30, a 16-year-old Guatemalan boy died after officials at an HHS detention facility noticed that he was sick. He was hospitalized in intensive care for several days before his death. He was then transferred to a crowded central processing center in the Rio Grande Valley, the busiest transit route for migrants along the border. It also recently opened a 500-person tent near one port of entry and announced plans to open another.
Amnesty International asked "how many deaths it will take for the administration to ensure the safety and security of children".
"It is unsafe and cruel to detain people, particularly children, in crowded and unsanitary conditions for seeking protection", it added.