Earlier this month Cake went head to head with M&C Saatchi Sport & Entertainment in a final pitch for the account.
Initially five agencies pitched for the work.
Cake worked with the airliner last year on a six-month project, #flightdecks. The campaign celebrated the launch of Virgin's new fleet of Boeing 787s, by staging a live-streamed gig from 35,000 feet with music artists Rudimental and Gorgon City.
Simon Dornan, interim head of consumer PR at Virgin Atlantic, said: "We were looking for an innovative partner to work with long-term on building our brand, and Cake was the clear winner. The #flightdecks campaign showed us that Cake is a first-rate creative agency, backed up by a solid knowledge of the modern PR landscape."
Adrian Pettett, CEO of Cake Group, said: "Virgin Atlantic is a recognised global brand with a reputation for forward thinking and innovation."