For most of his life Baudouin de Courtenay worked at Imperial Russian universities: Kazan (1874–1883), Dorpat (now Estonia) (1883–1893), Kraków (1893–1899) in Austria-Hungary, and St. Petersburg (1900–1918).

He was born in Radzymin, in the Warsaw Governorate of Congress Poland (a state in personal union with the Russian Empire), to a family of distant French extraction.

In 1870 he received a doctorate from the University of Leipzig for his work on analogy and a master's degree from St. Petersburg for his Polish-language dissertation On the Old Polish Language Prior to the 14th Century.

Between 1894 and 1898 he occupied the same post at the Jagiellonian University in Kraków only to be appointed to St. Petersburg, where he continued to refine his theory of phonetic alternations.

In 1922, without his knowledge, he was proposed by the national minorities of Poland as a presidential candidate, but was defeated in the third round of voting in the Polish parliament and eventually Gabriel Narutowicz was chosen.

Throughout his life he published hundreds of scientific works in Polish, Russian, Czech, Slovenian, Italian, French and German.

Davies writes: "He was a pacifist, an advocate of the fight for environmental protection, a feminist, a fighter for progress in the field of education, and a free thinker, and he was against most of the social and intellectual conventions of his day.

[11] His daughter, Cezaria Baudouin de Courtenay Ehrenkreutz Jędrzejewiczowa was one of the founders of the Polish school of ethnology and anthropology as well as a professor at the universities of Vilnius and Warsaw.