The agency will work alongside the charity, fronted by British personalities including Lenny Henry and Davina McCall, for the next of its annual fundraisers, due to take place in March next year.
The agency was involved with Comic Relief activity earlier in the year when it attempted to give the knitted ITV Digital Monkey mascot, which was created for the failed platform by Mother, to the charity to avoid a lengthy custody battle between itself and the platform's administrators, Deloitte & Touche, over the rights to the toy.
Although these plans were immediately scotched by Deloitte, there is still some hope the deal might be allowed to go through.
Comic Relief's request marks the first time that it has enlisted the help of an advertising agency. Mother will work across a range of initiatives to help the charity as it looks to refresh its identity and keep itself relevant while simultaneously moving it forward. The strapline last year was: "Say pants to poverty."
The agency's two-pronged brief will involve encouraging the public to get involved in raising money before the event and by making donations on the day.
Mother's activity is unlikely to encompass a traditional advertising solution, with work running across a range of media.
Andy Medd of Mother said: "It's very modest about who it's involved with and what it achieves, but everyone loves Comic Relief and we're honoured to be asked."
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