John Brown is to end 12 years working his way up through the ranks at Agoda and step aside to a chairperson position.
He will be replaced by Omri Morgenshtern from July 1 this year.
Morgenshtern is currently chief operating officer at the Booking Holdings-owned, Asia Pacific-focused online travel agency.
He joined the business in 2014 as part of the acquisition of marketing startup Qlika by then-Priceline Group, where he was co-founder and CEO.
Following the purchase, he became senior product owner for algorithms and learning systems, before taking on the vice president of product development, chief product officer and then chief operating officer role from 2018.
Brown joined Agoda in 2010 as vice president, before making his way through the CPO and COO positions before becoming CEO in 2018, based in Bangkok, Thailand.
Glenn Fogel, CEO at Booking Holdings, says Morgenshtern has played a "a critical role in directing Agoda's product and service offerings."
"His knowledge and experience of the business is unmatched, and I look forward to Agoda's continued momentum under his leadership."