Villiger, who was FIFA’s Deputy Secretary General and Chief Legal and Integrity Officer, was one of the few senior members of previous FIFA president Sepp Blatter's administration who kept his position under his successor Gianni Infantino.
"I had the privilege to be part of FIFA in different roles with different responsibilities. After accomplishing a successful FIFA World Cup in Russia, the time for me has come to turn the page to a new chapter, seeking for new challenges”, said Villiger in a statement released by FIFA.
FIFA Secretary General Fatma Samoura said Swiss Villiger had been a "pillar of the organisation".
He came to the fore at FIFA following the 2015 FBI raid in Zurich which saw seven officials arrested on corruption charges.
With Blatter, who was later banned from football by FIFA's Ethics Committee, facing a separate Swiss investigation, Villiger, then head of legal affairs, worked closely with the U.S. law firm Quinn Emanuel Urquhart & Sullivan.
The firm conducted an internal investigation of FIFA and helped in relations with the U.S Department of Justice.
Blatter, who led FIFA for 17 years, has always denied any wrongdoing.
Praising Villiger, Samoura added: "I congratulate him wholeheartedly on his great career within FIFA, in which he has consistently demonstrated his expertise and professionalism, as well as his dedication to this great organisation.
"His competence earned him the trust and respect of internal and external stakeholders. I wish Marco all the best in his future endeavours."
Since Infantino was elected FIFA president, senior officials from the organisation have moved on with the Swiss keen to bring in his own staff.
More than 40 entities and individuals have been charged by U.S. prosecutors in connection with the FIFA investigation.
The probe has resulted in more than two dozen guilty pleas and one trial of three former soccer officials, two of whom were found guilty by a jury.
(Reporting by Simon Evans in Manchester, England; Editing by Ken Ferris)
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