Since gaining control of the club, Sir Jim Ratcliffe has implemented significant cost-cutting measures.
His restructuring has already led to 250 job losses, the removal of Sir Alex Ferguson as a club ambassador, and the cancellation of traditional staff perks.
A club spokesman said: “As part of the ongoing restructure of our operations, Jackie Kay is leaving Manchester United after almost 30 years of outstanding service to the club.
“Jackie started at Old Trafford in 1995 as an executive assistant through a period of historic success under Sir Alex Ferguson. In 2013 she moved to Carrington and served a succession of men’s managers, first as executive assistant and for the past 9yrs heading first team operations.
“In all her roles, she has demonstrated unwavering commitment and played a key part in the day-to-day life of Manchester United at Old Trafford, Carrington and on the road wherever the team was playing. We thank Jackie for everything she has done for the club and wish her the very best for the future. She will always be welcome at the club.”