The Aardman creation, which made its debut in the 1995 Wallace and Gromit film A Close Shave, triumphed in a poll of the best BBC children's characters though the decades.
The shortlist featured shows such as The Magic Roundabout, Paddington, Willo The Wisp, Teletubbies and In The Night Garden, from the 1950s to the current decade.
Shaun - who was given his own animated TV series in 2007 - knocked Postman Pat into second place.
The Greendale-based series was originally made in the 1980s, but new episodes, featuring the scrapes of the postman and his cat Jess, are still being produced.
Sooty and Sweep, the puppets who made their small-screen debut in the 1950s in The Sooty Show, came third.
The shortlist, of the top 50 BBC children's TV characters, was compiled by Radio Times and the BFI and sparked 41,000 votes.
Shaun the Sheep creator Richard Starzak said: "I'm chuffed, flattered and delighted, on behalf of everyone who has worked on Shaun the Sheep, for this honour.
"Many BBC animated characters were a big and important part of my childhood. It's amazing to think that Shaun will be part of so many people's happy memories. I'm so grateful to the readers of the Radio Times for voting for Shaun. You've made me very happy!"
Radio Times editor Ben Preston said: "Every generation has a favourite which lingers for a lifetime. Our winner, Shaun the Sheep, will be remembered in 50 years' time, just as the children of the 80s voted for Postman Pat, and Sooty and Sweep remain hugely popular almost 60 years after they were first broadcast.
"It's a testament to the enduring quality of British children's television that a contemporary character topped the poll in a shortlist filled with classic programmes from the last seven decades."
The results were announced as several children's shows, including Danger Mouse, Clangers Teletubbies and Thunderbirds are set for a comeback.
It has now emerged that Eighties show SuperTed is joining the list and also being remade.
Mike Young, who created the superhero, is part of the team who are in the early stages of making 26 new episodes and they want Melvyn Hayes and Derek Griffiths to resume their voice roles.
Young told Radio Times: "Popeye used to smash people in the face. And it was very funny. But of course there is no television network anywhere in the world that would let you do that now.
"In SuperTed, we had a gun-slinging cowboy, a flamboyantly gay skeleton and a fat guy who had jokes made about his weight. And all these things you just wouldn't do today. But you can still write the show in a funny, entertaining way."
:: Favourite BBC children's TV character:
1. Shaun the Sheep
2. Postman Pat
3. Sooty and Sweep
:: Most popular BBC Children's TV character by decade:
1. Sooty and Sweep (1955)
2. Captain Pugwash (1957)
3. Bill and Ben (1952)
1. The Magic Roundabout
2. Camberwick Green (1966), Trumpton (1967), Chigley (1969
3. Clangers (1969)
1. Paddington Bear (1975)
2. The Wombles (1973)
3. Bagpuss (1974)
1. Postman Pat (1981)
2. Pingu (1986)
3. Willo the Wisp (1981)
1. Bob the Builder (1998)
2. Teletubbies (1997)
3. Brum (1991)
1. Shaun the Sheep (2007)
2. Sarah and Duck (2013)
3. In the Night Garden (2007)