Bobrowski was born in Tilsit in East Prussia. In 1925, he moved first to Rastenburg, then in 1928 on to Königsberg, where he attended the humanist Gymnasium. One of his teachers was Ernst Wiechert. In 1937, he started a degree in art history in Berlin. As a member of the Confessing Church, Bobrowski had contact with the German resistance against National Socialism. He was a lance corporal for the entire Second World War in Poland, France and the Soviet Union. In 1943 he married Johanna Buddrus.

From 1945...1949 Bobrowski was imprisoned by the Soviet Union, where he spent time working in a coal mine. On his release, he worked as an editor in Berlin, first for the Altberliner Verlag, a children’s publisher run by Lucie Grosner, and then from 1959 for the Union Verlag publishing house. His work was influenced by his knowledge of Eastern European landscapes and of the German and Slavic cultures and languages, combined with ancient myths. In 1964, Bobrowski became a member of the PEN Club.

In East Berlin in 1965, Brobowski died as a result of a perforated appendix. Since 1992, the Foundation for Prussian Maritime Trade (Stiftung Preußische Seehandlung) has donated funds towards the Johannes Brobowski Medal.