A media agency partner has yet to be confirmed on the business.
WCRS's appointment will see the brand return to advertising after an absence of four years in a bid to re-establish its credentials as the UK's leading sandwich chain. The company faces competition from rival sandwich chains, such as Greggs and Benjis.
WCRS's appointment will cover advertising, design and in-store branding, and forthcoming work will run across a variety of media.
Stephen Woodford, the chief executive of WCRS, said: "Pret a Manger is one of the UK's most powerful new brands. We are delighted to be reunited with them to face an exciting future together."
The agency originally won the Pret a Manger account in 1996 after a pitch against Young & Rubicam.
Pret a Manger was established in 1986 by the ex-City workers Julian Metcalfe and Sinclair Beecham. The company is now 33 per cent-owned by McDonald's and has 115 outlets in UK cities, employing 2,200 staff.