The Port was established to service the East Kimberley cattle industry pioneered by the Durack family and others. It was gazetted as a Port in 1886, with vessels berthing at a jetty at Antons Landing - the remains of which can be seen at low water at the northern end of Foreshore Drive near the museum.

In 1917, a new timber jetty was built on the site of the current jetty to service the newly opened meat works. This jetty was positioned to make use of a natural deep water basin to allow for larger, deep draft ships. In the early 1970’s the current steel and concrete jetty was built to replace the original timber structure and the unique horseshoe shape was completed allowing the more efficient movement of cargo on and off the jetty. Originally, a light rail loop was used to move cargo from the jetty to the meat-works and storage sheds, one of the original trains can be seen at the front of the port administration building. Up until the 1980’s, frozen meat was exported from Wyndham to overseas markets. Since the closure of the meat works in 1986, live cattle exports have become a major trade for the Port.

Since the early days of European settlement, Wyndham Port has played a major role in connecting the East Kimberley to the outside world. In the early years, when road transport was non-existent, the only way to get people or goods into the area was by ship. Stateships, the government owned shipping line, operated a regular service from Fremantle to Wyndham from 1908 to 1995. This was replaced by a government-subsidised service which was discontinued in late 2013. A container sea freight service into the Region, as an alternative to road transport, is still considered to be a vital service to the East Kimberley. A number of shipping providers are investigating options to deliver a service that links Wyndham to SE Asia and/or Darwin.

After over 100 years of government control, in 1999 the operation of the port was awarded to the Ord River District Co-operative LTD (now CGLtd) under an Operating Agreement of three terms of five years each with the Department of Planning and Infrastructure. This contract was extended through to June 30 2019.