Bajer entered the Danish army but was discharged when it was reduced after the 1864 war with Prussia. He then started working for the emancipation of women, for the peace movement, and for Scandinavian cooperation. He was a founder of the Danish Women's Association in 1871 and established in 1882 the Association for the Neutralization of Denmark, which was renamed the Danish Peace Association in 1885.

A left-wing liberal member of the Danish Parliament (1872–95), Bajer advocated international arbitration treaties and considerably influenced the development of the Danish neutrality policy. He was a prominent delegate to the first Scandinavian peace conference (1885) and provided great impetus for the formation of the International Peace Bureau in Bern in 1891; he was president of the Bureau until 1907.