The process, which was led by AAR, kicked off in November last year. The incumbent was AKQA.
AnalogFolk will oversee brand activation, social media and content marketing work.
The shop’s data division, AnalogFolk DNA, will oversee "optimised business solutions, data science and automation, and predictive analytics and insight".
Wieden & Kennedy Amsterdam and Mindshare hold Booking.com’s creative and media accounts respectively.
Ash Choudhury, the global digital brand director at Booking.com, said: "AnalogFolk are the perfect partners to help take us into the next chapter of the Booking.com success story.
"Their deep understanding of our business, data-driven strategic and creative innovation and sheer passion set them apart."
In July last year, Booking.com encouraged consumers to make the most of their summer by "winging it" on everything but their holiday. The online film was created by Wieden & Kennedy Amsterdam.