Challenger Harbour is a marina in Fremantle, Western Australia, situated adjacent to the Fremantle Fishing Boat Harbour.

Originally constructed between 1983 and 1984 to host racing yachts for the 1987 America's Cup, it has since been modified for recreational vessels.

It is considered the largest small boat harbour in Western Australia, comprising public boat pens, jetties, and a connecting boardwalk.

The harbour takes its name from HMS Challenger, the vessel commanded by Captain Charles Fremantle when he raised the British flag at Arthur Head — at the mouth of the Swan River — on 2 May 1829, marking the founding of the Swan River Colony.

A stone breakwater protects the harbour from ocean swells. The location offers convenient access to the Indian Ocean and nearby destinations including Rottnest, Penguin, and Carnac Islands.