Not being the firstborn, he started a military career in 1581 and joined the Eighty Years' War as part of the entourage of Alexander Farnese, Prince of Parma, another Italian serving in the Spanish armies, under whom he participated in operations like the capture of Sluis and the relief of Paris.

He stationed himself in his native Sicily, joining the galley squad of Martín de Padilla in 1604, and temporarily serving as governor of Messina under Viceroy Juan Gaspar Fernández Pacheco.

In 1611, d'Aragona convinced the Duke of Osuna, the new Viceroy of Sicily, to appoint him commander of his galley fleet, replacing the absent and notoriously uncooperative Pedro de Gamboa y Leyva.

d'Aragona had his first showing for him in 1611, when he was part of an armada led by Álvaro II de Bazán to sack the Kerkennah Islands, near Tunis, and the following year he participated in an attack to Djerba teaming up with Genoese and Tuscan ships.

d'Aragona earned the reputation of a unbeatable commander, which he lived up to in Samos by destroying the fleet of Sinari Pasha in the Battle of Cape Corvo in August 1613.