St. Hedwig’s Church was built in the 18th century following a request from local parishioners to King Frederick II. He donated the land on which the church was built. The church was dedicated to the patron of Silesia and Brandenburg, Saint Hedwig of Andechs. It was the first Catholic church built in Prussia after the Reformation.The building was designed by Georg Wenzeslaus von Knobelsdorff  and modelled after the Pantheon in Rome. Construction started in 1747, but interrupted and delayed several times by economic problems. It was not opened until 1 November 1773, when the king’s friend, Ignacy Krasicki, the Bishop of Warmia (later Archbishop of Gniezno), officiated at the cathedral’s consecration.
After the Kristallnacht pogroms that took place on the night of 9–10 November 1938, Bernhard Lichtenberg, a canon of the cathedral chapter of St Hedwig since 1931, prayed publicly for Jews at evening prayer. Lichtenberg was later jailed by the Nazis and died on the way to the concentration camp at Dachau. In 1965, Lichtenberg’s remains were transferred to the cryptat St. Hedwig’s.
The cathedral was severely damaged by allied bombing in an air raid on 1 March 1943. Only the damaged shell of the building was left standing. Reconstruction started in 1952 and on 1 November 1963, All Saints’ Day, the new high altar was consecrated by the Bishop of Berlin, Alfred Cardinal Bengsch.