Stickelberger was born in Buch in the canton of Schaffhausen into a family of a pastor. He graduated from a gymnasium in 1867 and studied next in the University of Heidelberg. In 1874 he received a doctorate in Berlin under the direction of Karl Weierstrass for his work on transformation of quadratic forms to a diagonal form. In the same year he obtained his Habilitation from Polytechnicum in Zurich (now ETH Zurich). In 1879 he became an extraordinary professor in the Albert Ludwigs University of Freiburg. From 1896 to 1919 he worked there as a full professor, and from 1919 until his return to Basel in 1924 he held the title of a distinguished professor ("ordentlicher Honorarprofessor"). He was married in 1895, but his wife and son both died in 1918. Stickelberger died on April 11, 1936 and was buried next to his wife and son in Freiburg.