Managing director Karen Smart has quit after eight years, Manchester Airport Group said.
Deteriorating scenes at the airport had led Manchester mayor Andy Burnham to call for emergency services to be stationed there to control crowds.
MAG chief executive Charlie Cornish said: “Over the last two years, Karen has guided Manchester Airport through the most challenging period of its 84-year history, having made a major contribution to MAG throughout her time with the business.
“I am sorry to lose Karen after her years of valuable service, but also understand her desire to return to the South for family reasons and indeed to explore new career opportunities.”
Ian Costigan will take on the role of interim managing director in charge of a recruitment drive to solve ongoing issues ahead of the summer.