It will create campaigns to promote games titles including Metroid Prime, which launches on March 21.
Nintendo's work was previously handled by Leonardo, the digital arm of above-the-line agency Leo Burnett UK.
UK marketing controller Dawn Paine said Lateral had been appointed to create all online ad campaigns that are in the pipeline, but added that Leonardo might be used on specific projects.
Nintendo's PR agency, Cake, will continue to develop viral marketing campaigns through its digital offshoot, Cake New Media.
Nintendo is preparing a £6.9m ad blitz across Europe to promote the GameBoy Advance SP, which launches on March 28. It will target an older audience than the existing GameBoy Advance.
Lateral worked for Xbox alongside Agency Republic at the end of last year to relaunch the console's brand experience web site, playmore.com.
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