Rubuta ci gaba don wannan sakin layi - An rarraba sashen zuwa sassan Czech da Jamusanci a 1882, kuma Faculty of Natural Sciences ya zama cibiyar daban tsakanin 1920-1939. A shekara ta 1939, sojojin Nazi na Jamus suka rufe makarantar, kuma aka tsananta wa malamai da ɗalibai. Bayan ƙarshen mamayar a 1945, Faculty of Arts ya sake bunƙasa na fewan shekaru; wannan ya ƙare da ƙarfi a cikin 1948 ta juyin mulkin kwaminisanci a cikin 1948. Darajar kwalejin ta ragu da sauri sakamakon tilasta barin malamai da yawa da aka girmama da kuma gabatar da karatun Marxist-Leninist. A cikin shekarun 1960, sannu a hankali sashen ya fara buɗewa ga fitattun masu tunani na lokacin, amma wannan yanayin ya canza ta hanyar mamayar Soviet a cikin 1968
, wanda Jan Palach, dalibi na kwalejin, ya yi zanga-zangar ta hanyar ƙona kansa. Bayan ƙarshen mulkin kwaminisanci a Czechoslovakia a 1989, da kuma barin wakilansa a cikin sashen, an sake kafa shi a matsayin ɗayan manyan jami'o'in kasar da aka fi daraja.