He was born at Karlsburg Castle, in Durlach (now part of Karlsruhe) as the son of Friedrich V, Margrave of Baden-Durlach and Barbara of Württemberg.

The imperial army of Emperor Leopold I began to organize a common defense against the Turks and demanded that Baden-Durlach should also provide troops.

The Emperor granted, even before the war began, to Frederick and his cousin, Margrave William of Baden-Baden, the right to use the style Serene Highness.

This title was hereditary until 1803, when Margrave Charles Frederick of the in 1771 re-united margraviate of Baden was raised to Elector after he had greatly expanded his territory during the German Mediatisation.

Frederick VI married his first wife on 30 November 1642 Christine Magdalene (born: 15 May 1616; died: 14 August 1662), the daughter of the Count Palatine John Casimir of Kleeburg.