The business, which was previously handled in-house, plans to boost the marketing push behind the PJ brand and its range of smoothies.
St Luke's has been tasked with creating a TV campaign for the brand.
Peter Knowles, the marketing advisor at PJ Smoothies, said: "PJ is market leader in a growing category, but there's tough competition out there.
We are looking for a long-term brand partner to help us cement our position and St Luke's demonstrated the quality of thinking that we are confident will help us achieve this objective."
PJ's first advertising campaign broke in July last year. Using the theme "done being bad", it included TV, outdoor and sampling activity.
Liz Little, the business development director at St Luke's, said: "We look forward to working with the team to develop some exciting creative work that fully exploits this."
The appointment does not affect PJ's media agency, Pure Media, which will continue to handle all the brand's planning and buying.