Hussain, who won 2015's Great British Bake Off, will judge alongside chef and food writer Allegra McEvedy.
CBBC's Junior Bake Off sees 40 youngsters aged nine to 12 competing for the title.
Hussain said: "This time last year I was in the Bake Off tent and now I get to go back and help encourage the next generation to get their bake on."
The contestants will each complete two bakes over 10 heats, including a technical bake and showstopper challenge, with four youngsters in the grand final.
The CBBC show's previous judges have included Mary Berry, Paul Hollywood, James Martin and Graham Hornigold.
Hussain, 31, has built a career since winning Bake Off which includes her first cook book, a column for The Times and a request from Buckingham Palace to make a cake for the Queen's 90th birthday. She will also present The Chronicles of Nadiya, a TV show tracing her culinary roots in Bangladesh.
She won last year's final on BBC One after baking a "big fat British wedding cake" adorned with jewels from her own wedding day as the showstopper.
It became the most-watched TV programme of the year with an average audience of 15.1 million people, according to consolidated figures, which include catch-up viewing.
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Former Bake Off winner Nadiya Hussain has said she is "excited" to be joining the show's junior version as a judge.