Cytomegalovirus infection after a heart transplant is a recurrent medical condition. Its frequency increases when the donors are serum-positive, and the recipients are serum-negative to this virus. In the pediatric population, the infection only develops in a small percentage and the patients rarely present resistance to conventional treatment with ganciclovir and valganciclovir. We presented the first report of a pediatric case of the cytomegalovirus infection resistant to ganciclovir and valganciclovir after a heart transplant in a Peruvian public hospital with an unusual presentation. The resistance to these drugs was evident after 277 days of evolution of the disease considering the non-remission of the symptomatology and the persistence of an elevated viral load. The administration of foscarnet led to a clinical and laboratory improvement until remission of the disease.