The agencies take over the account after a final shootout against incumbent agencies J Walter Thompson and MindShare.
Mother and Naked will be working with a team of other agencies on the Boots account, including MediaCom, which will be handling the media buying while Naked handles planning.
Below-the-line the business moves out of JWT agency Black Cat and into Craik Jones. Poke, Cake and Circus have also been awarded work as part of the Mother led team.
Mother founder Stef Calcraft said the win was a huge one for Mother and builds on another highly successful new business year for the hot shop with wins from Coca-Cola and Archers.
"It's not just about Mother. It is about Mother, Naked, Mediacom, Craik Jones, Saturday, Poke, Cake and Circus and a visionary client," said Calcraft. "Thought leaders each and every one. This is the future and the new client and agency team will do great things together for Boots."
Last week Boots cut the shortlist for the account to two, dropping Publicis and Abbott Mead Vickers BBDO from the review.
The loss of the account is a blow for incumbent agency J Walter Thompson, which will now be looking for a retail account to replace Boots, adding to the DIY retailer B&Q it picked up earlier this year.
David Kneale, Boots chief commercial officer, who is responsible for marketing following the axing of marketing director Ann Francke mid- way through the review, said the decision was a tough one after a long relationship with JWT and Mindshare.
"As we now move into a new era of modernising our business and making it more compelling for our customers, we're greatly excited by the opportunity of working with the Mother team who have shown a real grasp of our current and future communication needs throughout the pitch process. Also, all four agency teams tackled the pitch with great energy and we appreciate all their hard work," said Kneale.
Francke left Boots after less than a year in the job and the appointment of Kneale meant that Boots would have no-one with sole responsibility for marketing.
Francke was axed as part of a management shake-up initiated by new chief executive Richard Baker.
Boots most recent activity was the launch of its £10m Christmas campaign by JWT that claims Boots has something for everyone.
If you have an opinion on this or any other issue raised on Brand Republic, join the debate in the Forum here.