He was the only son of Don Pedro Fajardo, 1st Marquis of Los Vélez by second wife Dona Mencía de la Cueva.
He married in 1526 Dona Leonor Fernández de Córdoba, daughter of the 3rd Count of Cabra, who also died in 1575.
He was the ancestor of the 1st Baron of Castellvell de Rosanés and 1st Marquess of Martorell in 1627 Don Luis Francisco Fajardo de Zúñiga, Requeséns y Girón, ?th Lord of the Majorat of Martorell in Catalonia, son of the 5th Marquesses of los Vélez.
He was the 2nd Marquis of los Vélez Grandee of Spain First Class with a Coat of Arms of Fajardo, 2nd Count of Gagliano, 4th Count and Lord of the City of Cartagena and the 8th Lord of Alhama, Mula, Librilla, Molina de Segura, La Puebla[disambiguation needed], etc.
He was Adelantado-Mayor and Captain-General / Captain-Major of the Kingdom of Murcia and Granada, Captain-General of the Kingdom of Granada, where he was the first to enter with his Army on 4 or 6 January 1569, Alcalde of Lorca, Knight and Commander of Caravaca and Thirteen (Trece) in the Order of Santiago.