The agency beat DDB London to the prize in a final shoot-out after Mother and Delaney Lund Knox Warren were knocked off the shortlist last month.
Incumbent agency Saatchi & Saatchi pulled out of the pitch in March shortly after the review was announced.
The agency had held the account since 2000, during which time it retained the 'Exceedingly good cakes' line created by J Walter Thompson in the 1970s.
It went on to develop the brand's most recent campaign featuring Mr Kipling as the man who makes cakes so good he can be forgiven for anything else.
One Saatchi spot for Mr Kipling's mince pies featured a realistic childbirth scene during a Nativity play, which was deemed to be in breach of the advertising code after 797 people complained.
The review was called following Simon Foster's appointment as head of marketing for Mr Kipling and Lyons Cakes later this year.
WCRS's appointment does not affect media agency Universal McCann's hold on RHM's £10m planning and buying account.
Earlier this week Manor Bakeries-owner RHM said it planned to boost marketing spend for its Mr Kipling and Cadbury cakes brands after announcing a £45m windfall for its Manor Bakeries cake producing business.
A statement from the firm said that marketing investment for the two brands will "significantly increase" as part of a drive to develop both existing and new products.
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