The agency won the account following a three-way pitch handled by Creativebrief. A review of the business, which was handled by incumbent Euro RSCG, launched in January.
Beta will be responsible for evolving CityJet's £1m 'Now We're Flying' campaign, launched last September by Euro RSCG.
A new campaign for CityJet, a subsidiary of Air France, will be rolled out in the summer across TV, digital and direct, pushing the airline's key business routes.
Andre Cini, commercial director, CityJet, said: "The creative campaign we developed last year gave us a distinct look and feel.
"However, the challenge now is to take the brand in a different creative direction that will not only resonate with our core customers, but that will also build traction with a new audience who has perhaps not considered flying with CityJet before.
"We believe Beta has the creative energy to deliver that new audience."
Garry Lace, founding partner at Beta, said: "CityJet operate in the most competitive and exciting aviation market in the world, which gives us enormous scope and potential to deliver a number of compelling creative campaigns."
Beta will work alongside CityJet's incumbent media buyers, 7Stars, and PR and social media agency, Consolidated PR.