The comedian will be voicing the 26-part cartoon series. Richard Curtis, Mr Bean co-creator and writer of Notting Hill and the Vicar of Dibley, is also closely involved in the new project.
The star of the live-action series is being filmed for each new 30-minute show so the animators can replicate Atkinson's unique movements for the cartoon Mr Bean.
As with the original series, the animated version will have little dialogue.
Mr Bean will be joined by in the cartoon by faithful sidekick Teddy, evil landlady Mrs Wicket and her horrible one-eyed cat Scrapper.
"While the new series will remain entirely faithful to the original feel of Mr Bean, in animation we can do all sorts of things that I'm physically restricted from in live action," said Atkinson.
"It'll be Bean, but more so - visiting places we have never been able to reach before."
Claudia Lloyd is series-producing the show for Tiger Aspect Productions, with original Mr Bean lead writer Robin Driscoll heading the writing team on the animated version.
Tiger Aspect is working in collaboration with London-based animation studio Richard Purdum Productions and Budapest-based Varga Studios to produce the new cartoon Mr Bean.
The show is due to go out on ITV later this year.
Ms Lloyd said: "With Purdum's unique eye for detail and Varga's vast experience and skill in animation, we aim to create a modern animation classic for all age groups."
Pearson Television International will be selling a series of 52 11-minute versions of the animated Mr Bean to broadcasters outside the UK.
The live-action Mr Bean show won an International Emmy and a Montreaux Golden Globe and the 14 episodes have been sold to more than 150 countries.
Bean - the Ultimate Disaster Movie made more
than £165m worldwide.
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