The app, which has been created by Christian group Exodus International, offers news, information and resources from the organisation that claims to address "unwanted same-sex attraction" through counselling. It's only available in the US.
More than 88,000 web users have signed a petition against the "hateful and bigoted" content contained with the app.
The petition also raises concerns that Apple awarded the app a 4+ rating, which means it contains "no objectionable content".
"Apple might consider thinking about its customer base and the penchant many lesbian and gay people have for ethical consumerism when endorsing an offensive app like this," Ben Summerskill, chief executive of gay rights group Stonewall, told The Guardian.
Apple has yet to comment on the issue.
Last year, the tech company withdrew a similar app called Manhatten Declaration after a petition calling for its removal gained 8,000 signatures.
See also: Wikileaks app removed from App Store