The game which was uploaded in 2013 but only surged to the top in downloads earlier this year was removed early today.
The success of the game that based its appeal on being simple and also maddeningly difficult made its creator Nguyen Ha Dong, 29, a minor celebrity.
The game was downloaded more than 50 million times on App Store alone. In an interview with The Verge website, Mr Dong said Flappy Bird was making 50,000 US dollars (£30,000) a day in advertising revenue
But tech blogger Carter Thomas said the sudden popularity of Flappy Bird might have been due to use of fake accounts run by computers to create downloads and reviews.
Mr Thomas said he could not prove his suspicion and that the success of Flappy Bird might also be explained by it being "just a wildly viral game".
Mr Dong, from Hanoi, wrote on Twitter on Saturday that the Internet sensation caused by the game "ruins my simple life" and he now hated it.
"I will take Flappy Bird down. I cannot take this anymore," he wrote.
He did not address the inflated downloads allegation but denied suggestions he was withdrawing the game because it breached another game maker's copyright.
"It is not anything related to legal issues. I just cannot keep it anymore," he wrote.