Xavier was born in Granada, Nicaragua, a son of Pedro Joaquín Chamorro Zelaya and his wife Margarita Cardenal Argüello.Chamorro's great-grandfather was Pedro Joaquín Chamorro Alfaro, 39th President of Nicaragua.

Xavier had two brothers, Jaime and Pedro Joaquín, who succeeded their father as publisher of La Prensa newspaper.

Prior to 1980, Chamorro Cardenal had worked with La Prensa, a well-known Conservative publication.

In 1980, he left La Prensa, taking eighty percent of the staff with him, as they favored the Sandinistas.

They had five children together: Francisco Xavier, Margarita, Gabriel, Ana María, and Juan Sebastián.