The seven-minute show, beginning on Wednesday, will turn the works of five prominent indigenous artists into a permanent part of the city's skyline.
The show, Badu Gili, means "water light" in the language of the site's traditional owners, the Gadigal people.
Organisers say it celebrates time-honoured stories with contemporary art.
"It combines music and images to create a gateway to Australia's First Nations history and culture for the 8.2 million people who visit the opera house each year," said curator Rhoda Roberts.
The animation features works by Jenuarrie (Judith Warrie), Frances Belle Parker, Alick Tipoti, Lin Onus and Minnie Pwerle.
It will debut at 17:45 local time (07:45 GMT) on Wednesday.
Spectacular art installations most recently lit up the opera house for Vivid Sydney, a light festival.
A vibrant animation telling stories of indigenous Australia will be projected on to the Sydney Opera House every night at sunset.