The agency did not state why the teenager was detained for a week but said he was "due for placement" in a facility for youth operated by the US Department of Health and Human Services.
The incident happened less than a week following the death of a two-year-old child after he and his mother were detained by the Border Patrol.
According to the US and Guatemalan authorities, the small child died after several weeks in the hospital. Officials, at that time, were quoted as saying that the boy was suffering from very high fever and difficulty in breathing, and was later diagnosed with pneumonia at a children's hospital.
"Four in six months is a clear pattern of willful, callous disregard for children's lives," Jess Morales Rocketto, chair of the advocacy group 'Families Belong Together' told Al Jazeera.
All five children who lost their lives after being apprehended by the Border Patrol so far were from Guatemala, a Latin American nation ravaged by organised crime and extortion, poverty, rampant corruption, and political turmoil.
More than 114,000 people from Guatemala have been apprehended by the Border Patrol between October and April.
In early in December last year, a seven-year-old Jakelin Caal Maquin died of a bacterial infection under the US custody at the border.
An eight-year-old Felipe Gomez Alonzo died on the Christmas Eve of a flu infection. He had been detained with his father for a week before falling sick.
After Gomez Alonzo's death, the Department of Homeland Security announced it would expand medical checks and ensure that all children in Border Patrol custody would receive "a more thorough hands-on assessment at the earliest possible time."
Juan de Leon Gutierrez, 16, died on April 30 after officials noticed that he was sick at a youth detention facility operated by US Department of Health and Human Services.
The medical examiner in Corpus Christi, Texas, said Juan had been diagnosed with a rare condition known as Pott's puffy tumour, which can be caused by a severe sinus infection or head trauma.
President Donald Trump's administration has for months warned that the US immigration system was at a "breaking point." The administration has asked for USD 4.5 billion in emergency humanitarian funding and urged Congress to change laws that would allow agencies to detain families longer and deport them more quickly.