The 300-passenger ferry will run five times a day between the Barrack Street Jetty and Fremantle B Shed between July 13 and 17, and again between July 31 and August 4.
The Fremantle Line will be closed from 7pm on Friday until the first service the following Thursday to allow the new Fremantle Line Tunnel to be connected.
The first ferry service will leave Barrack Street at 5.30am with the last leaving Fremantle at 7.15pm. The non-stop trip will take just over one hour.
Public Transport Authority spokesman David Hynes said Fremantle Line passengers would be the worst affected during the closures.
‘We suggest that those who do use the ferry might find they enjoy a change in their regular commute,’ he said.
During the five-day works, Joondalup Line trains will terminate at Leederville with rail replacement buses operating to Perth. For more information, visit transperth.wa.gov.au.