Werner II of Habsburg (died 19 August 1167) was Count of Habsburg also called Werner III and a progenitor of the royal House of Habsburg. He was the great-great-grandfather of King Rudolph I of Germany.

Werner II, Count of Habsburg
Reign	8 November 1111 - 19 August 1167
Died	(1167-08-19)19 August 1167 near Tusculum
Noble family	House of Habsburg
Spouse(s)	Ida of Homberg
Issue	Albert III, Count of Habsburg Otto II, Bishop of Constance
Father	Otto II
Mother	Hilla of Pfirt

He was the son of Count Otto II of Habsburg and Hilla of Pfirt. Werner married Ida of Homberg. He is known for having been involved in the War of Bregenz Succession of 1164 – 1166.

He died near Tusculum after the Battle of Monte Porzio.

He was the father of Count Albert III of Habsburg and Bishop Otto II of Constance (1165–1174). His daughter Richenza married Count Louis I of Pfirt.