Zacharias Papantoniou's term of office was interrupted by his death in February 1940. Two months later, the painter and conservator Georgios Stratigos (1876-1944) took over as the National Gallery’s director, but his office was also cut short when he died in November 1944. On 26 August 1945, the archaeologist Dimitrios Evanghelidis (1886-1959) temporarily took over as director, remaining in this position until 28 February 1947. On 1 March 1947, he was succeeded by the archaeologist and art historian Nikolaos Bertos (1885-1949), whose tenure was also interrupted by his death on 11 January 1949.

During the War and the German occupation, the main concern was to safeguard the artworks, which were transferred to the Archaeological Museum and the most valuable among them to the Bank of Greece treasury. In the meantime, since January 1941, the Gallery had been forced to move out of the main NTUA building, which was requisitioned to host a military hospital for the wounded and later used by the German occupation army. Its premises were immediately re-occupied by the NTUA, on the grounds that the number of students and therefore the teaching needs had increased. Thus, the Gallery was temporarily housed in the Benaki Museum, followed by successive relocations to Casa d’ Italia and the Archaeological Museum, where the art collections were transferred in 1948.

The museum’s limited operation in the 1940s only permitted minimal enrichment of the painting collection. Nevertheless, in 1946, the Gallery received a very generous donation. Odysseas Fokas, a ‘curator’ (conservator) since 1915, bequeathed his movable and immovable property ‘for the enrichment of the international modern art section’. His bequest made Fokas the second great benefactor, following Alexandros Soutsos.

In addition, after the Liberation, a substantial donation of French artists’works was made – in tribute to the Greek people’s heroic stance during the German occupation – an idea put forth in 1942 by intellectual and literary figure Roger Milliex and his companion, Tatiana Gritsi-Milliex. It comprised 28 paintings, 6 drawings, 6 engravings, 4 sculptures and 2 books, delivered to the National Gallery in July 1949.