Sultan Muzaffar Shah II (1546–1570) was the second Sultan of Johor. He was known as Raja Muda Perdana before he succeeded the throne. He was installed to the throne of Johor in 1564 by the Acehnese upon the death of his father, Sultan Alauddin Riayat Shah II, who died shortly after he was captured and brought back to Aceh after the Acehnese invasion of Johor.