The Extra about kids' lives in Afghanistan after the war took the prize for Best Factual Programme.
Former Newsround presenter Matthew Price, who was the reporter in the programme, said he was really happy to win.
"It was probably the story of the year in many ways," he said at the bash. "I just feel really proud to be part of this film. It means a lot, I'm very excited."
Monsters, Inc
Cat Deeley gave Matt Baker his best presenter prize
Other big winners were SM:tv, which won Best Entertainment Series, and also won the Lego/Bafta Kids' Vote.
There was a big surprise in the Best Film vote when both Harry Potter and the Philosopher's Stone and Lord of the Rings: Fellowship of the Ring were beaten.
Monsters, Inc. beat both films - and Stuart Little 2 - to win the award.
And in a four-way CBBC battle between to win best presenter, Matt Baker beat fellow Blue Peter presenter Konnie Huq, as well as Angellica Bell and Ortis from Short Change.
Hear story
All the kids' Bafta winners
