iPhone and iPad users can no longer download the software, which was produced by Living Hope Ministries (LHM) - a Texas-based group offering one-on-one pastoral counselling and mentoring.
A petition was started by the gay rights group Truth Wins Out which accused the app of saying gay, lesbian, bisexual and transgender people are "sick".
The organisation's executive director Wayne Besen said: "We thank Apple for exemplifying corporate responsibility and taking swift action to remove a dangerous app that stigmatizes and demeans LGBT people.
"Ex-gay programmes are consumer fraud and cause significant harm to the people they purport to help."
Founded in 1989, LHM describes its mission as to "proclaim God's truth" and promote "sexual and relational wholeness".
Its website goes on to say: "LHM proclaims a Christ-centred, biblical world-view of sexual expression rooted in one man and one woman in a committed, monogamous, heterosexual marriage for life.
"Anything less than this ideal, falls short of God's best for humanity."
Apps found to contain "defamatory, discriminatory, or mean-spirited" content - including such references to sexual orientation - face being penalised under Apple's app rules.
Ricky Chelette, the executive director of LHM - which is not related to a UK-based church of the same name - told NBC News the app - which has been available for years - is a "discipleship ministry" and "very much like a church."
He added: "We help people understand who they are in Christ. We only help those individuals who are seeking us."
Truth Wins Out is now urging Amazon and Google to remove Android versions of the app.
Premier has contacted Amazon, Apple, Google and LHM for a comment.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.