Mr Godwin will be responsible for all aspects of CBeebies and CBBC - the children's channels enjoyed by millions of children each week.
He has spent the past 20 years working in children's media - both inside and outside the BBC - and is currently head of news, factual and entertainment for BBC Children's, responsible for key shows such as Newsround, Blue Peter, Serious, TMI and The Slammer.
Mr Godwin is expected to take up the post next month, replacing Richard Deverell, who moves up to be chief operating officer for BBC North.
The role will be based at Salford Quays from 2011.
The appointment comes at a time when children's programming in general is in decline, a point raised by Ofcom in a recent report about the future of public service broadcasting.
Manchester has traditionally been a strong centre for children's television production - particularly in animation - and it will be hoped that the department's move here might provide a fillip for the sector. Starting his career at the BBC in 1986, and spending five years at Nickelodeon before returning in 2005, Mr Godwin has vast experience in children's media.
He has produced Blue Peter and directed Saturday morning classics Going Live and Live & Kicking, as well as heading Children's BBC continuity. At Nickelodeon, he was head of original production, and became responsible for all online and interactive content.
Since returning to BBC Children's as head of entertainment, Mr Godwin has been executive producer of many CBBC shows, including the BAFTA award-winning The Slammer and Chucklevision.
Mr Godwin said: "As someone who joined the department 20 years ago as a trainee, I can't think of a more exciting challenge, or greater honour, than to lead the brilliant people who make CBeebies and CBBC.
"The fact that we're soon to become part of BBC North in Salford makes it even more exciting."
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