Ernst Walter Zeeden was born in Berlin as the son of regional court director Konrad Zeeden (1879–1925) and his wife Marianne. After he earned the Abitur at the Goethe-Gymnasium in Berlin, he studied history, German and Latin at the universities of Leipzig, Heidelberg, Munich and Freiburg. In Leipzig he was a member of student organisation Corps Saxonia Leipzig. In 1939, he earned a doctor's degree (Dr. phil) with his thesis Hardenberg und der Gedanke einer Volksvertretung in Preußen 1807–1812 under the supervision of Gerhard Ritter. On November 4, 1948, he married Pauline Dubbert in Freiburg. They had five children.
