The boy's death follows those of two other Guatemalan migrant children in December.
A 16-year-old Guatemalan migrant died Tuesday in a Texas hospital while in the custody of the U.S. government on Wednesday after his health steadily declined due to a severe brain infection, according to officials from both countries.
He entered the United States near the border city of El Paso, Texas and was detained by U.S. border patrol agents on April 19, according to a statement from Guatemala's foreign ministry.
The boy was then sent to a shelter nearly 1,130 kilometers away in Brownsville, the statement added, where he was "beginning the process of family reunification."
He ultimately underwent surgery to relieve pressure in his head, according to the ministry.
The unnamed teen was from Camotan, a town near Guatemala's border with Honduras known for high levels of malnutrition among a mostly poor population that ekes out a living as farmers.
The teenager was transferred on April 20 from Immigration and Customs Enforcement (ICE) custody to the Brownsville shelter run by the Office of Refugee Resettlement, which houses migrant children.
"Upon arrival to the shelter the minor did not note any health concerns," the U.S. government claimed in a statement. The next morning the boy "became noticeably ill including fever, chills and a headache," according to the statement.
Shelter staff took the teen to a hospital emergency department that morning but he was released to the shelter the same day, the statement added.
The boy's health did not improve and the next day he was taken to another hospital emergency department by ambulance. Later that day he was transferred to a children's hospital's intensive care unit in Driscoll, Texas, where he stayed for several days before he died.
Human rights advocates and Democrats in Congress have called for better medical screening in border facilities to detect such cases sooner and prevent deaths.
The U.S. officials said the cause of the teenager's death is under review and the case will be subject to a full review.