From August 1370 Joanna travelled to Prague, where she was married on 29 September 1370 to Wenceslaus, son and heir of Emperor Charles IV by his third wife, Anna of Swidnica.

The conjugal bond suited the Luxembourg ruler to strengthen ties with the Bavarian duke, who held extensive estates in the Low Countries; nevertheless, Joanna was not the first choice of a bride for Wenceslaus.

Charles had his son elected King of the Romans in 1376 and upon his death in 1378, Wenceslaus also inherited the Kingdom of Bohemia.

The marriage lasted for sixteen years, however the couple had no children (it is said that Wenceslaus was infertile due to his alcoholism).

Joanna died in 1386 at the age of thirty or thirty-one,[2] allegedly from the consequences of an attack by Wenceslaus' hunting dogs.