It is the second time this month an immigrant child has died while being detained after crossing the US-Mexico border.
The previous instance saw a seven-year-old girl, also from Guatemala, die hours after being taken into custody.
US officials said she had tried to cross the Mexico-US border illegally with her family.
The Guatemalan girl, who authorities there named as Jakeline Caal, died of dehydration and shock, the Washington Post reported. Border officials were quoted as saying she had not had food or water for several days.
Photo caption: Migrants arriving at the US-Mexico border say they are fleeing persecution, poverty and violence