Following the incident, tensions between Guatemala and Belize over a border dispute have risen sharply.
Guatemala responded Friday with a scathing statement lamenting the Belizean military´s "aggressive attitude," saying its "acts of violence" are hurting bilateral relations.
Belize accuses Guatemala of "amassing" troops along the border.
Guatemala says the 13-year-old boy was attacked by Belizean soldiers. Belize says its troops shot in self-defence after coming under fire.
Belize`s government said the Guatemalan teenager was shot dead on Wednesday in the Cebada area of the Chiquibul National Park, on the western border with its larger neighbour.
Guatemala said the incident happened in a community which is on the border between the Guatemalan department of Peten and Belize. Guatemalan President Jimmy Moralles later described the incident as a "cowardly and excessive attack", and called for those responsible to be brought to justice.
According to the AFP news agency, Defence Minister William Mansilla said Guatemala had deployed 3,000 troops on the border. "It is a preventive measure, it is not a declaration of war," he was quoted as saying.
Meanwhile, Belize´s government said Mr Moralles´ comments were "inflammatory". Belize said its patrol came under fire and was forced to shoot back in self-defence.
Guatemala´s claim to parts of territory governed by its neighbour dates back to when Belize was a British colony
The territorial dispute between the two Central American nations dates back more than 150 years. Belize became independent in 1981; however Guatemala did not recognize it for another decade because of the land dispute.
Earlier this week, Luis Almagro, the head of the Organization of American States, visited both countries in an effort to resolve the situation.