He will spend a day attending the naval spectacle in Sydney, which features more than 40 warships, 16 tall ships and 8000 naval personnel from 19 nations.
The prince last visited Australia in 2003 during a gap year break when he worked on a ranch in the outback.
Harry will be a guest of honour at the nine-day event on October 5, which marks the centenary of the arrival of the Royal Australian Navy's first fleet in Sydney Harbour in 1913. The prince will also visit Perth, the capital of Western Australia.
Kensington Palace said further details about his programme would be announced at a later date.