Christian was the son of Duke William of Schleswig-Holstein-Sonderburg-Beck (and after 1825 Duke of Glücksburg). He entered the Danish army in 1835, serving in the Schleswig War (1848–50). In 1842 he married Louise of Hesse-Kassel, cousin of the childless Danish king, Frederick VII, and he was named successor to the throne of Denmark, Schleswig-Holstein, and Lauenburg in the London protocol of 1852. When Christian came to the throne at Frederick's death in November 1863, he was forced by popular feeling in Denmark to sign the November constitution, which incorporated Schleswig into the state and made war with the German states inevitable.

In the years after the disastrous war of 1864, Christian IX supported conservative minority governments against the ever-expanding democratic forces in Denmark. He finally submitted to them in 1901 by appointing a majority cabinet. This change brought full parliamentary government to Denmark.