McMillan, who is CEO of operator AGS Airports Ltd, has decided to relocate to Australia with her family, and is set to leave her post in early 2018.
McMillan has also served as managing director of Glasgow Airport for over nine years.
AGS Airports shairman, Sir Peter Mason, said: “On behalf of the AGS Board, I would like to convey our sincere thanks to Amanda for the outstanding job she has done in establishing the AGS Airports Ltd group since its creation in 2014.
“Through her distinctive brand of leadership, AGS has become one of the UK’s leading airport groups.
"During this period, our airports in Aberdeen, Glasgow and Southampton have benefited hugely from her drive and commitment to continually improve the customer experience for our growing number of passengers.
McMillan noted: “I have thoroughly enjoyed leading AGS Airports. It is with mixed emotions that I am planning to move on, but this opportunity is one that comes at the right time for us as a family.
"I am immensely proud of the team at AGS which has delivered significant passenger growth, secured new carriers, built enviable destination lists and completed a series of first-class modernisation projects.”