Aby Warburg died in 1929, four years before the threat became undeniable. His colleagues—led by Fritz Saxl, who had joined the institute in 1913 and served as its first director—made the decision to move the library to safety. In 1933, with Lord Lee of Fareham, Samuel Courtauld, and the Warburg family providing support, the collection was shipped to London and installed in Thames House. In 1934. The move preserved tens of thousands of volumes and a photographic archive of enormous scholarly value. In 1937 the institute moved to the Imperial Institute Buildings, and in 1944 it was formally incorporated into the University of London. A research institute formed around a single scholar's obsession had found institutional permanence in a country that was not its own.

The building on Woburn Square in Bloomsbury was designed by Charles Holden and built in 1957. It sits within the University of London's Bloomsbury campus, adjacent to Birkbeck College and the School of Oriental and African Studies. Inside, the library holds more than 350,000 volumes—almost all kept on open shelves, accessible without special permission. But what makes the library distinctive is not its size. It is the arrangement. Warburg devised a classification system based on his division of human history into four categories: Action, Orientation, Word, and Image. Books are shelved by subject within these categories, placed near other books with which they have unexpected affinities. The system is designed to produce the kind of accidental encounters between ideas that Warburg believed scholarship required.

The scholars associated with the Warburg Institute constitute a remarkable roll call of twentieth-century humanistic scholarship. Ernst Cassirer, the Neo-Kantian philosopher, used it in Hamburg. Erwin Panofsky, who transformed art history with his iconographic method, worked there. Ernst Gombrich—who directed the institute from 1959 to 1976 and wrote The Story of Art, one of the most widely read books about art ever published—was a Warburg scholar. Frances Yates, whose research into Renaissance magic and occult philosophy opened entirely new areas of historical inquiry, worked at the Warburg for decades. Rudolf Wittkower's work on architectural proportion, Edgar Wind's studies of Renaissance allegory—these foundational texts of twentieth-century art history were produced in this building on Woburn Square.

For most of its London history the Warburg Institute was a specialist research institution with restricted access. In 2022, work began on a major renovation branded 'Warburg Renaissance.' The project created a new structure in the former courtyard, with a lecture theatre and improved storage for archives and special collections. The renovated building opened to the wider public in September 2024, featuring an exhibition focused on the institute's history and an installation by ceramicist Edmund de Waal called Library of Exile—a work about books that have been displaced from their places of origin. It was a fitting subject for a library that had itself been a refugee. The institute also holds 450,000 photographs of paintings, sculptures, prints, and drawings, and maintains the archive of Aby Warburg's personal papers alongside those of Henri Frankfort and Ernst Gombrich.