In 1937, after the occupation of Peking by Japan, universities were forced to either change, close down or move to another area. Because of the special nature of Fu-Jen, however, it was permitted to operate basically unchanged, and thus continued to work among young people in China. In 1944 the Japanese arrested many teachers and students for anti-Japanese activities.
民國廿六年七七事變，北平陷入日寇之手，當時北平各大學，或變質、或關閉、或流亡，而「輔仁」則以其直屬教廷的關係，得以維持校務；在淪陷區中，為延續民族教育的神聖工作，和日本軍閥周旋。