He was an illegitimate son of Gonzalo Pizarro Rodríguez de Aguilar (senior) who as colonel of infantry served in the Italian campaigns under Gonzalo Fernández de Córdoba, and in Navarre, with some distinction. His mother was Francisca González Mateos, a woman of slender means from Trujillo. Through his father, Francisco was second cousin to Hernán Cortés, the famed conquistador of Mexico.