With the coming signs of war, he was offered positions by many other universities - from Warsaw, Rome, Paris, London and New York City - but refused. After the German and Soviet invasions of Poland in 1939, Vilnius was occupied by the Soviet Union. Professor Pelczar helped the Polish Red Cross provided care for thousands of refugees. In 1941 after German invasion of the Soviet Union, he continued to help various refugees, among them, Jews hiding from the Nazis, and working with medical services of Polish resistance organization Armia Krajowa. At night, from 16 to 17 September 1943, he was arrested by the Lithuanian Security Police ('Sauguma') in a standard retaliatory actions against the Armia Krajowa, whose members on 15 September assassinated a Lithuanian Gestapo collaborator, member of Lithuanian security police, Marianas Padabas. Out of 100 arrested members of Polish intelligentsia, 10 were randomly selected and executed on the morning of September 17, becoming ones of the 100 000 victims who died in Ponary. Professor Pelczar was among them, along with fellow professor of the Stefan Batory university, Mieczysław Gutkowski, 2 Polish army officers, 3 officials, a lawyer and 2 engineers. A day later an order from Germany ordered his release - but it was too late.