The movie, directed by Gore Verbinski, will be honoured at the festival's gala ceremony on 24 October (11) in Beverly Hills.
Depp voiced the titular lizard character in the film, which also featured Isla Fisher, Abigail Breslin, Alfred Molina, Bill Nighy, Harry Dean Stanton, Ray Winstone and Timothy Olyphant.
Announcing the news of Rango's latest honour, Carlos de Abreu, the founder and executive director of the Hollywood Film Festival, says, "It is a great pleasure to recognise Rango as the recipient of our animation award. This piece of cinematic treasure borders on surrealism and Rango will be a classic for generations to come."
Past recipients of the Hollywood Animation Award include Cars, Ratatouille, Toy Story 3, UP and Wall-E.