In 1941, the college was closed down due to the break of the second World War. During the war in 1943, under the Japanese Administration after the loss of the British, the College was turned into a Japanese school for the locals. It did not receive much support from the public, due to the Japanese failure to recognize the college as a 'special' school. As the number of students continue to decline, the Japanese decided to close it down and the college was converted into a Japanese Civil Service Headquarters, which witnessed the prosecutions of hundreds of people at the Rugby Field.

The year 1945 saw another change in the college as it was turned into a Japanese hospital, as the Japanese began to suffer from huge losses in their campaigns in the Pacific and Asia. It saw the influx of countless of patients, resulting from battles into the college. After the historic atomic bombing of Hiroshima and Nagasaki, the surrender of the Japanese signalled another process in the college evolution, as it bear the Union Jack again on its helm.

The British apparently was not attentive to the needs of the people after the war. In August 1946, the College was still closed, and no sign of it being reopened. When Sir Carey, the former headmaster arrived to reclaim his position in the college, he saw that the college was in such a sorry state with blood stains on the walls, damaged army tents and neglected huts around the college compund. Murmurs of dissatisfaction went on, though it came to no avail.

The first move to repair and redevelop the college was initiated by a group of concerned old boys, who organized a fund to support their deed. And it was well received by the public, who evidently wanted the college to have its glory days back. However, due to the lack of funds, the bricks were painted yellowish white for the first time. The reopening of the college took its place in 1947, when adopted its present motto, which will forever be associated with the school, 'FIAT SAPIENTIA VIRTUS', the Latin for 'Let Manliness Come Through Wisdom'.

Dato' Onn bin Jaafar, an old boy, then the Chairman of UMNO, in line with the reopening of the college, persuaded the British to increase the number of students admitted, giving opportunity to Malays regardless of their family background, to live up to the real objective of its establishment. Thus, since then, the once afluential royals gradually dissapeared, to give way to the emergence of a new breed of outstanding Malay students in the college. And in 1948, the Form Six classes were started.

The King's Pavillion was borrowed to the College in 1950. Two years after that, the King's Pavillion was permanently given to the college by Sir Gerald Templer. In 1953, a significant moment in college history was written down as the first and probably the last girl was admitted to the college, as the college was the only mean to continue her studies in Britain.

In the year 1955, College celebrated its' Golden Jubilee in pomp and splendour as the College benefited from the vast devolopment on its' grounds. The Big School wings, The New School, Hargreaves Hall and other facilities were constructed. The ceremony was officiated by Sir Donald McGillivray, High Commissioner of Malaya and witnessed by all the nine rulers of the Malay States.

The College was made into a fully secondary school six years later. King's Pavillion was also returned to the government and turned into The Government English School. In memory of the building which was affectionately remembered by the boarders, The Pavillion was constructed as a new residential block in 1963.

Malay College's first Malay principal, Encik Abdul Aziz replaced NJ Ryan during the College's 60th anniversary.