The museum's visiting vessels program has brought some popular attractions to Darling Harbour.

The largest in scale and impact was the Netherlands-built replica of the 17th century Dutch East India Company flagship Batavia. The original Batavia was wrecked on Houtman Abrolhos, off the coast of Western Australia, in 1629. The Australia Netherlands Chamber of Commerce brought the superb replica to the museum in 2000 for Sydney's Olympic Games year.

Other spectacular visiting vessels have included the Australian-built replica of Duyfken, the first known European ship to visit Australia, a Soviet Foxtrot submarine and a replica Viking ship.