SFA compliance officer Clare Whyte will quit her role in the New Year.
The governing body have announced the legal enforcer is set to pursue a "new opportunity".
Whyte replaced Tony McGlennan in the role back in August 2018.
She has since overseen a number of high-profile disciplinary incidents and will remain until early 2021 to help ease her successor into the role.
An SFA statement said: "The Scottish FA can confirm that Clare Whyte will leave her role as compliance officer to take up a new opportunity.
"Clare will remain in post until early in the New Year to ensure a smooth handover period with her successor."
Hampden chief Ian Maxwell thanked Whyte as he paid tribute to her "professionalism and resilience" in the high-pressure role.
He said: “I would like to thank Clare for her commitment to the role over the past two years with the Scottish FA.
“In what is a high-pressure position in a relentless environment, she has shown professionalism and resilience.
“We will begin the process of recruiting a replacement in early course.”
Last year, MailSport revealed the compliance officer role had been under scrutiny for several months following a proposal put forward by a high-powered working group including Celtic and Rangers.
A number of disciplinary matters arose during Whyte's first season in the role, which led to a summit between officials and managers in January 2019.
Rangers had earlier been hauled into the dock following a scathing assessment of ref Willie Collum's performance during a clash with St Mirren.
But further controversy during a bad tempered derby against Celtic in April 2019 led to both clubs facing SFA charges for failing to control their players and staff.
That same season, then-Hearts boss Craig Levein copped a ban for criticising ref Bobby Madden.
In June this year, Whyte opened a probe against the Jambos and Partick Thistle over a joint legal bid to have their relegation overturned.
The clubs were later fined £2500 each.
