The veteran newsreader will receive the honour, which recognises an "outstanding and exceptional contribution to television", at Sunday's ceremony.
"This is a magnificent surprise," McDonald said. "I am honoured and absolutely delighted to join such a distinguished list of previous recipients."
Meanwhile, BAFTA's TV committee chair John Willis said: "No journalist and presenter is better loved and respected by the audience than Sir Trevor McDonald. His authority and humanity has shone through all his work. He is a very worthy recipient of the Fellowship because, for many years, he has been simply the best."
Stars who have previously been awarded the Fellowship include Dawn French, Richard Curtis, Bruce Forsyth and Jennifer Saunders. Melvyn Bragg was honoured last year.
The Philips British Academy Television Awards will be held at Grosvenor House in London on Sunday. The ceremony will also be broadcast on BBC One.
> In Full: BAFTA Television Awards 2011 nominees