Juan Pizarro was the illegitimate son of Captain Gonzalo Pizarro y Rodríguez de Aguilar (senior) (1446–1522) and María Alonso, from Trujillo. His father was a colonel of infantry who had served with distinction in the Italian campaigns under Gonzalo Fernández de Córdoba, and in Navarre. Juan Pizarro was the half brother of Francisco and Hernando Pizarro, and full brother to Gonzalo Pizarro.