The agency will manage the snack company's Nik Naks and Wheat Crunchies brands, previously held by Bartle Bogle Hegarty and Quiet Storm respectively.
Last year, JWT picked up the brief to relaunch Golden Wonder's main crisp brand, with the majority of the advertising concentrated in Scotland and Northern Ireland.
This latest appointment arrives on the back of that campaign, which saw sales grow by more than 20 per cent.
Golden Wonder is now believed to be putting £25 million into promoting its three core brands in the UK to compete with rival Walkers.
The Snack Factory bought the Nik Naks, Wheat Crunchies and Golden Wonder Crisps brands in 2001 in a £300 million deal.
Matt Drury, the managing partner on the Golden Wonder account, said: "Nik Naks has seen steady growth, and has huge potential. With its pungent flavour, irregular shape and reclusive nature, the brand is the great eccentric of the snack market. We are looking forward to introducing more people to its charms."
The Nik Naks brand was launched in 1983 and grew to become a national brand without major above-the-line support. It currently sponsors Channel 4's The Osbournes.