Pagan began his military career during the 1620-1622 Huguenot Rebellion and was promoted by Louis' first chief minister and his relative, the Charles d'Albert, duc de Luynes.

Among other actions, Pagan took part in the 1627/1628 Siege of La Rochelle, whose loss resulted in the 1629 Peace of Alès, ending Huguenot self-government within France.

France also became involved in the 1628-1631 War of the Mantuan Succession, in opposition to the Spanish-backed candidate; in March 1629, Pagan was part of a force that stormed barricades blocking the Pas de Suse, an act celebrated for its courage.

Pagan was promoted Maréchal de camp in 1642 and assigned to the Portuguese army but before taking up this post, he was blinded in an accident, ending his military career.

Pagan was invited by the Knights Hospitaller to submit a proposal for fortifying their base at Malta; this does not appear to have been accepted but in 1645, he published Les Fortifications.

These were then upgraded by French engineers, including Jean Errard (1554-1610) and Antoine de Ville (1596-1656); unlike them, Pagan's work was almost entirely theoretical but his background in geometry and mathematics allowed him to apply their concepts in a more structured way.