The Deichtorhallen is situated at a historically important site. Originally this was the location of the Berliner Bahnhof, the counterpart to the Hamburger Bahnhof in Berlin. After the new Hauptbahnhof was built, ​​construction began on the Deichtormarkt here in 1906. Initially featuring only a provisional roof, in 1911 construction began on the enclosed halls that now host major international exhibitions.

Despite their large size, the buildings soon no longer sufficed as market halls for the rapidly growing city of Hamburg. After the relocation of the wholesale market, from 1963 to 1984 the halls were used for a wholesale flower market. However, they increasingly fell into disrepair.

Finally the Hamburg industrialist Kurt A. Körber ensured their preservation. The Körber Foundation funded their restoration and handed over the renovated buildings to the city of Hamburg in 1988 on the occasion of the 800th anniversary of the city harbor. Since then, they have been managed by Deichtorhallen Hamburg GmbH, whose aim is to promote the visual arts, with a focus on the twentieth and twenty-first centuries.

On November 9, 1989, the show Einleuchten by Harald Szeemann marked the opening of the international exhibition program at the Deichtorhallen. In 2005, the House of Photography opened in the south hall. The opening exhibition Martin Munkácsi: Think While You Shoot! was curated by the founding director Prof. F.C. Gundlach.

The first director of the Deichtorhallen from 1989 to 1990 was Erik Berganus. Beginning in 1991, under the direction of Dr. Zdenek Felix the Deichtorhallen became a world-renowned art institution. From 2004 to 2008, Prof. Dr. Robert Fleck was director. Since 2009, Prof. Dr. Dirk Luckow has served as director of the Deichtorhallen Hamburg alongside Commercial Director Bert Antonius Kaufmann.

The House of Photography and the Hall for Contemporary Art were joined in 2011 by the Falckenberg Collection branch in Hamburg-Harburg. Since the opening in 1989, international artists have been presented in around 115 group exhibitions and 135 solo shows. In total, more than 250 major exhibition projects have been realized with works by over 2350 different artists.