Born in Wiener Neustadt, Frederick was the second surviving son of the Babenberg duke Leopold VI of Austria and Theodora Angelina, a Byzantine princess.

Frederick secondly married Agnes of Merania in 1229, an heiress of the extinct noble House of Andechs whose dowry included large possessions in Carniola and the Windic March.

Proud of his Byzantine descent, the young duke soon was known as the Quarrelsome because of his harsh rule and frequent wars against his neighbors, primarily with Hungary, Bavaria and Bohemia.

Not only had the duke refused to appear at the 1232 Reichstag diet in Aquileia, appealing to the Austrian Privilegium Minus privileges, and displeased the emperor by picking quarrels with King Béla IV of Hungary, he furthermore seemed to be involved in his brother-in-law Henry's conspiracy.

When he again refused to attend the 1235 diet in Mainz, Emperor Frederick II finally ostracized him and gave permission to King Wenceslaus I of Bohemia to invade the Austrian lands.

Vienna opened its gates for the united Bohemian and Bavarian forces and during the years of Frederick's ban even became an imperial free city, where the emperor had his son Conrad IV elected King of the Romans in 1237.

He and his knights managed to defeat a small Mongolian raiding party during the initial stages of the Battle of Mohi, but they soon left after inter-conflicts with King Bela IV and the Cumans in the region.

A minor raiding squadron started pillaging Wiener Neustadt in Southern Vienna, but Duke Frederick together with his knights and foreign allies, defeated them and drove them out.

The conflict with Bohemia was settled by the engagement of his niece Gertrude of Babenberg with King Wenceslaus' eldest son Margrave Vladislaus of Moravia.

Duke Frederick's ambitious plans were dashed when he died at the Battle of the Leitha River, in another border conflict he had picked with the Hungarian king Béla IV.

Shortly after the death of her uncle, Gertrude first married her fiancé Vladislaus of Moravia, who nevertheless died in the next year, then Margrave Herman VI of Baden, who did not manage to maintain his position in Austria, and finally in 1252 Prince Roman Danylovich, a younger brother of Knyaz Lev I Rurik, son-in-law of the Hungarian king, who also ended in divorce in 1253.