Werner Kaegi (1901–1979) was a Swiss historian. He is best known for a single work, a biography of Jacob Burkhardt. This appeared in seven volumes, from 1947 to 1982.
He was recipient of the Gottfried-Keller-Preis and the Erasmus Prize.
He had for wife the catholic mystic and stigmatist Adrienne von Speyr (1902–1967). Her spiritual director and friend, the theologian Hans Urs von Balthasar, kept a journal during many years about her life in which details regarding her relationship with Werner Kaegi can be found. This journal was later edited in 3 volumes under the name "Erde und himmel" ("Earth and heaven").
Kaegi became a foreign member of the Royal Netherlands Academy of Arts and Sciences in 1948.