Werner II of Habsburg (died 19 August 1167) was Count of Habsburg and a progenitor of the royal House of Habsburg. He was the great-great-grandfather of King Rudolph I of Germany.
He was the son of Count Otto II of Habsburg and Hilla of Pfirt. Werner married Ida of Homberg. 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.