The lyceum building was also damaged in the air raid targeted at the town on 2 February 1940. After Sortavala became part of the Soviet Union through the peace treaties after the Winter War, the lyceum building, too was returned to school use in 1940, when a komvuz or college producing specialists in agriculture established in Petrozavodsk in 1930 was transferred to the building.
After the end of the Winter War, the Sortavala Lyceum was closed. The teachers were transferred to educational institutions in different parts of Finland, and the students enrolled in schools throughout Finland. After the reoccupation of Sortavala, grammar schools, too, gradually returned to Sortavala, and in October 1942 the lyceum and the girls' school began their operations, now in the buildings of the Sortavala seminar. In academic year 1943–1944, students in grade 5 were formed into a co-educational class. In autumn 1944, when the Finns left Sortavala for good, the Sortavala Lyceum was transferred to Seinäjoki. There the school began operations as the Seinäjoki Lyceum, with Dr Uuno Karttunen as its principal for the academic year 1944–1945.