Andrew, chief executive of the group that owns the trade-only Gold Medal and Travel 2 brands, took up the role in December 2005.
Dnata is also parent to the Global Travel Group consortium, as well as OTAs Travel Republic and NetFlights. It is in turn owned by UAE state-backed Emirates Group.
Andrew will be replaced in the interim by Steve Allen, dnata divisional senior vice-president UAE airport operations.
A dnata spokesperson told TTG: “dnata confirms that Iain Andrew, divisional senior vice-president for dnata Travel, has resigned from the company.
“His replacement will be announced in due course.