The 82-year-old musician, painter and all-round TV personality will be handed the honour, recognising "outstanding and exceptional contribution to television", at the Royal Festival Hall in London on Sunday, May 27.
Upon learning of his recognition, the Aussie legend simply said: "I'm hugely honoured and very thrilled."
Chairman of BAFTA, Tim Corrie, commented: "Rolf Harris is one of the world's most iconic entertainers. He has huge audience appeal across multiple generations."
Apart from his singing and didgeridoo playing, he has enjoyed a TV career spanning almost 60 years.
Signing for the BBC in 1953, the star has captured the public's imagination fronting do-it-yourself drawing shows Rolf on Art and CITV's Cartoon Club.
Fondly recognised for his catchphrase, "Can you tell what it is yet?", his career on the small screen culminated with The Queen by Rolf - a Rolf on Art special showcasing his painting of Queen Elizabeth II for her 80th birthday in 2006.
Past winners of the Fellowship include Sir Bruce Forsyth, Dawn French, Richard Curtis, Jennifer Saunders and Melvyn Bragg. Sir Trevor McDonald took home the gong last year.
Dara O'Briain will host the BAFTA ceremony on BBC One.
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Photo gallery - Rolf Harris in pictures: