The pitch, handled by Agency Insight, also included Mother and Delaney Lund Knox Warren & Partners in its early stages. The incumbent, Saatchi & Saatchi, dropped out of the running soon after the pitch was announced.
The win follows news that Manor Bakeries' parent company, RHM, is set to boost marketing spend for its Mr Kipling and Cadbury cakes brands.
The strategy is part of a drive to develop both existing and new products.
Robin Wight, the chairman of WCRS, said: "We are very excited to have been selected and to have the opportunity to work with Manor Bakeries on the re-invigoration of such a famous British icon and to help with delivering its high growth aspirations for Mr Kipling."
Kate Taylor, the marketing director for Manor Bakeries, added: "It was a very difficult decision at the end. Both agencies fielded highly competent teams but WCRS just had the edge. We are looking forward to getting down to work with it."
WCRS will work alongside Mr Kipling's media agency, Universal McCann.
Saatchis has held the Mr Kipling account since 2000. It retained the "exceedingly good cakes" line created in the 70s by J. Walter Thompson but re-invented Mr Kipling as the "man who made cakes so good you'd forgive him for anything".
A Saatchis' Christmas campaign showing a woman giving birth during a nativity play provoked 797 complaints and led to Manor Bakeries taking it off air. Saatchis will continue to work on Manor Bakeries' Cadbury's cakes business.