The child had been in the hospital in US custody for several weeks after entering the US with her mother, Posten reported and quoted Guatemala Consul Tekandi Paniagua and another source.
CNN has reached out to the Home Security Ministry and Guatemalan Consul in Del Rio, Texas, but has not yet received a reply.
The boy would be the fourth Guatemalan child since December to die after a border view.
The first two deaths led to congressional hearings, and immigration authorities have ordered an increase in medical controls for children in their storage.
Homeland officials and CBP have announced new procedures, including additional medical controls of all children, focusing on children under 10 years of age.
CBP began reviewing its policy in December, especially focusing on taking care of young children, both at intake and beyond 24 hours in storage, the agency said.