Originally founded as a Roman Catholic mission station by Father Richard Docherty in 1935 at Werntek Nganayi (Old Mission), Wadeye was later relocated 14 kilometres inland to its current site. The township was formerly known as Port Keats, a name still used by some residents and visitors today.
The mission quickly became a central gathering place for surrounding tribes. However, limited space and resources led to conflict among groups seeking to join. Father Docherty had to restrict entry until the mission’s facilities and gardens could sustain more people.
Over time, the mission became home to people from seven language groups and more than 20 clans. The Australian Government managed the mission until the late 1970s, when local governance was transferred to the Kardu Numida Council in 1978. It was then that the community was officially renamed Wadeye.