Whyte is currently a Procurator Fiscal Depute for the Crown Office and Procurator Fiscal Service.
She also has wide experience in grassroots football, but will also undergo a handover period with the outgoing compliance officer later this month.
The Scottish FA chief executive Ian Maxwell told 'Sky Sports': "I am delighted that we have been able to appoint someone with Clare's credentials to what is an important role within the Scottish FA."
"It's also a vital position within Scottish football as a whole that comes with its own unique challenges and pressures and I am convinced Clare will be an asset to the organisation and the game in this country."
"I would also like to take the opportunity to thank Tony for his excellent work over the last four years with the Scottish FA."
"Tony has worked tirelessly to modernise a judicial system we can be proud of."