A member of an illustrious Swedish family, Per the Younger was the grandson of Per Brahe the Elder—a nephew of the Swedish king Gustav I Vasa—who was created the first Swedish count and wrote historical works and Oeconomia (1585). The younger Brahe fought under the command of Gustav II Adolf in the Thirty Years' War in Prussia (1626–28), becoming a colonel. He was elected marshal of the nobility in 1629 and appointed a privy councillor in 1630. While serving as a member of Queen Christina's regency council (1632–44), he helped negotiate the Truce of Stuhmsdorf (1635) with Poland.

As governor general of Finland (1637–41, 1648–54), Brahe reformed the administration, promoted commerce, communications, and agriculture, and sponsored the building of many new towns. He founded the University of Åbo (Turku) in 1640 and acted as its chancellor from 1646 until his death. While serving as lord high chancellor (1641–80), he also exerted great influence as a member of the regency council (1660–72) for Charles XI. Brahe's brother Count Nils Brahe also served with distinction under the command of Gustav II Adolf before falling in battle at Naumburg in Saxony in 1632.