Chief operating officer Gilthorpe will take up her new role on 1 May after 15 years at Heathrow.
Javier Echave, Heathrow’s chief financial officer, will take over from Gilthorpe as COO from 26 April.
Sally Ding, Heathrow’s director of treasury and corporate finance, will deputise for Echave while a permanent recruitment process gets under way.
Heathrow hailed Gilthorpe’s contribution to the airport’s development and successes since she joined in 2006 as "immense".
"Emma has consistently delivered positive outcomes in challenging circumstances demonstrating incisive decision-making, strategic thinking and an engaging leadership style that has made her a successful and leading figure across stakeholders," said Heathrow.
"Emma hands over an operation to Javier that is back to its best after the challenges of the past few years."
Echave, meanwhile, has been credited by Heathrow for shaping the airport’s business plan, securing its financial position and playing a leading role embedding sustainability in the finance sector.
Thomas Woldbye, Heathrow’s chief executive, said: "Over the last 15 years, few have played a more instrumental role in shaping Heathrow’s success and building our great culture than Emma Gilthorpe.
"She will be missed by all of us at Heathrow, and I’m personally very sad to see her leave. The Royal Mail are lucky to have secured such an outstanding leader to take them forward.
"Emma leaves behind an operation that is performing well, and Javier’s effective leadership style and deep understanding of our business will help the operations team continue to make every journey better. In the meantime, Sally’s capable hands will look after our finances.
“We wish Emma all the best in her new role outside Heathrow, and to Javier and Sally in their new roles."
