He was the eldest son of Christian August, Duke of Schleswig-Holstein-Sonderburg-Augustenburg (1696–1754) and his wife Duchess Louise Frederikke née Countess af Danneskiold-Samsøe (1699–1744).

In 1754, his father died and Frederick Christian inherited Augustenborg Castle and Gråsten.

He waived his claims on the duchies of Schleswig and Holstein and in return the King of Denmark (who was also Duke of Schleswig and Holstein) granted him a favourable settlement.

This allowed him to purchase Als and Sundeved, making him the largest landowner in Schleswig.

Frederick Christian served as a general in the Danish army.