Andrae was born in Anger, near Leipzig, Germany. After finishing school at Gimma (the school of the princes of Saxony), he studied architecture for four years at the Technical University in Dresden. Andrae was only twenty-three when, In 1898, he set off for the Near East with the Deutsche Orient-Gesellschaft's Babylon Expedition. In Babylon Andrae learned excavation techniques from the expedition's leader, Robert Koldewey, the most prominent excavator of that time. In 1903, Andrae undertook the first excavation of his own, at Aššur, the capital of Assyria. He worked there until 1914. Andrae also worked at Shuruppak (modern Fara) and Kisurra (Abu Hatab), both south of Babylon, and at Hatra, the Parthian city of the sun god northwest of Aššur.
During World War I, Andrae served as a German army officer in the Near East. After the war he was employed by the Berlin Museum, where he succeeded Koldewey as curator of the Near East collection. In 1928 he became director of the Near East department of the State Museum of Berlin, a position he held until the 1950s. After World War II, Andrae became a professor of the history of architecture at the Technical University in Berlin. Toward the end of his life, an accident caused his almost complete blindness.
At Aššur, Andrae first introduced the system of examining levels: in the area of the Temple of Ishtar, the oldest building at Aššur, he named building levels by letter, designating A for the uppermost and H for the lowest level. He also developed Koldewey's methods of archaeological work for the coming generations. At the Berlin Museum, Andrae was responsible for the reconstruction work on the Procession Street, the Ishtar Gate, and other monuments from Aššur and Uruk.
- Andrae, Ernst Walter, and Rainer Michael Boehmer. Sketches by an Excavator: Walter Andrae im Orient, 1898–1919. Berlin, 1989.
- Andrae, Walter. Lebenserinnerungen eines Ausgräbers. Berlin, 1961.
- Andrae, Walter. Das wiedererstandene Assur. 2d ed. Munich, 1977.