Formula 1's governing body is to split with its interim secretary general Shaila-Ann Rao less than six months after appointing her.
An FIA statement said Rao had joined to assist new president Mohammed Ben Sulayem in his "transition period".
It said she was leaving because "this period is now coming to an end".
Sources close to Rao have told BBC Sport that the decision to leave was hers - she resigned because the FIA is going through a re-organisation process and she felt that there would not be a job in which she was interested at the end of it.
She will leave the FIA at the end of November.
Sulayem, who took over as FIA president in December last year, said: "Shaila-Ann has provided me with great support in respect to Formula 1, always acting with professionalism and integrity."
Rao joined the FIA in June from her previous post as special adviser to Mercedes F1 team principal Toto Wolff.
Her links to Mercedes caused concern at both Ferrari and Red Bull.
In particular, at the height of the cost-cap row, Red Bull raised questions about Rao and whether they had been targeted.
Red Bull team principal Christian Horner has said that it was Rao who called him shortly after Max Verstappen clinched his second world title at the Japanese Grand Prix to tell him officially that Red Bull had been found in breach of the financial regulations.
The FIA found Red Bull to have exceeded the $145m (£114m) cost cap by £1.86m. Their penalty was a fine of $7m (£5.9m) and a 10% reduction in their permitted aerodynamic research allowance.
Sulayem was asked about Rao's future at last weekend's Abu Dhabi Grand Prix. He hinted that she would be leaving the FIA, by saying: "Her position is interim secretary general. What does interim mean?"
But he added: "Shaila-Ann has been supportive a lot to me and I see her intelligence on big decisions. I will defend my people.
"When it comes to Shaila-Ann, there was an accusation that she is mainly a supporter of Mercedes.
"Actually, when the penalties were there, she said: 'It's a bit harsh.' And I said: 'My God, there is someone accusing her of being with Mercedes and she's saying to me that it's harsh.'"
MOTD Top 10 World Cup 2022: The most controversial moments rankedFrom old pick-ups to the fastest car on the planet: Top Gear tests a full range of vehicles