During World War I, on the invasion of Belgium by the Germans, Fredericq was active in encouraging the patriotic feelings of his countrymen in occupied Belgium and supporting non-violent resistance to the invader. As a result, he was deported to Germany on 16 March 1916, together with his colleague, the historian Henri Pirenne. He was interned successively at Gütersloh, Jena and Bürgel. The ordeal weakened him both physically and mentally.