Lucy Bird, the £100,000-a-year chief executive of Marketing Edinburgh, walked away last week, two months after the slogan angered local politicians and prompted derision from the public.
In October, the Sunday Herald revealed that Marketing Edinburgh, which is owned by the city council, was embroiled in a row over an attempt to rebrand the city.
The "Incredinburgh" catchphrase had been coined by The Leith Agency, which had been hired by Marketing Edinburgh to spearhead the £300,000 relaunch.
However, the city's leaders were furious about the strategy and the slogan was dumped after it was leaked to this newspaper on the eve of the launch.
Alan Johnston, chairman of Marketing Edinburgh, said: "This decision has been entirely Lucy's and while not desired the board understands her rationale and she leaves with our gratitude and best wishes."
One council source said the Incredinburgh row meant that Bird's resignation was inevitable, saying: "People said straight after that episode that she might have to consider her position. She never recovered from it."