1903-05 he was assistant to Walter Andrae in the acclaimed excavations of Assur, and later traveled widely in Iraq and Iran at the beginning of the twentieth century. He surveyed and documented many historical sites in Turkey, Syria, Persia (later Iran) and most importantly in Iraq (e.g. Baghdad, Ctesiphon). At Samarra he carried out the first excavations of an Islamic period site in 1911-13. After military service during World War I he was appointed full professor for "Landes- und Altertumskunde des Orients" in Berlin in 1920. This was the first professorship for Near/Middle Eastern archaeology in the world. 1923-25 he started explorations in Persia and described many of the countries´ most important ruins for the first time. In 1925 he moved to Tehran and stayed there most of the time until 1934. He was instrumental in creating a Persian law of antiquities and excavated in the Achaemenid capitals Pasargadae and Persepolis.
He left Iran at the end of 1934 for a year in London, but never returned. In 1935 he was forced, for racial reasons (he was of Jewish descent), to leave his position in Germany and became a faculty member of the Institute for Advanced Study from 1936 to 1944. He died in Basel, Switzerland in 1948.
The bulk of the Ernst Herzfeld Papers are housed in the archives of the Freer Gallery of Art and the Arthur M. Sackler Gallery, Smithsonian Institution, in Washington, DC. The material, some 30,000 documents include his field notebooks, photographs, drawings and object inventories from his excavations at Samarra, Persepolis, Pasargadae and elsewhere in Iran, Iraq, Turkey and Syria. The archives is open by appointment Tuesdays, Wednesdays and Thursdays, from 10 a.m. to 5 p.m. Other Herzfeld research materials, notes, photographs and drawings are at the Metropolitan Museum of Art, in the Departments of Islamic Art and Ancient Near Eastern art.
The archives are currently undertaking a monumental project to digitize all of Ernst Herzfeld's remaining squeezes. Over 400 of these delicate paper impressions of ancient monuments will be photographed from multiple angles to create online files that users can manipulate. The user will be able to adjust flash angle, contrast, magnification, and many other settings to make the squeezes readable. This project is planned to be completed in late 2010 and early 2011.
Literary works 
- Iranische Felsreliefs, 1910
- Archäologische Reise im Euphrat- und Tigris-Gebiet, 4 Vols., 1911-1920 (together with Friedrich Sarre
- Paikuli, 2 Vols., 1924
- Die Ausgrabungen von Samarra, 5 Vols., 1923-1930
- Archaeological History of Iran, (Schweich Lectures for 1934)
- Altpersische Inschriften, 1938
- Iran in the ancient East, 1940
- Zoroaster and his world, 2 Vols., 1947
See also 
Gunter, Ann C. / Stefan R. Hauser (eds.), Ernst Herzfeld and the Development of Near Eastern Studies, 1900-1950. Leiden: Brill 2005.
- Finding Aids for the Herzfeld Archive in the Freer Gallery of Art and Arthur M. Sackler Gallery, Smithsonian Institution, Washington DC.
- Ernst Herzfeld Papers Collections Search Center, S.I.R.I.S., Smithsonian Institution, Washington, DC
- Ernst Herzfeld Papers, Series 7: Records of Samarra Expeditions, 1906-1945 Freer Gallery of Art and Arthur M. Sackler Gallery, Smithsonian Institution, Washington DC.
- Ernst Herzfeld-Gesellschaft (Ernst Herzfeld Society for Exploration of Islamic Art and Archaeology).