The 49-year-old had been deported from Arizona. He was taken to a temporary hospital in Guatemala City.
On Thursday, three children who arrived aboard a deportation flight were placed under observation after they were found to be suffering from severe coughs, one of the symptoms of the virus.
Guatemala has expressed concern about deported migrants spreading the virus. Guatemala currently has 49 confirmed cases and one death, while the United States has about 278,000 cases and over 7,150 deaths.