More than 80,000 people have signed a petition against the so-called "gay cure" app, which Apple deemed to have "no objectionable content".
Exodus International, the pro-Christian group behind the app, promotes the "ex-gay" movement, encouraging people to change their sexuality. The app gives users "freedom from homosexuality through the power of Jesus", according to the group.
Apple had not returned a request for comment at the time of publication.
Ben Summerskill, chief executive of gay rights group Stonewall, said: "At Stonewall, we've all been on this app since 8am and we can assure your readers it's having absolutely no effect.
"Apple might consider thinking about their customer base and the penchant many lesbian and gay people have for ethical consumerism when endorsing an offensive app like this."
The technology giant is notoriously strict in deciding which apps it allows on to its popular iPhone and iPad handsets. Last year Apple withdrew a similar anti-gay iPhone app called Manhattan Declaration after Change.org, the online activism site, handed over an 8,000-strong petition."