In a statement, Barack Obama also acknowledged that many people would be struggling to come out about their sexuality, and that society's laws, as well as people, affect the way that's dealt with.
He was speaking in response to an online petition inspired by Leelah Alcorn, a 17-year-old American transgender teenager who committed suicide last December because of her Christian parent's refusal to acknowledge her identity as a woman.
120,000 people signed the petition within three months. [include link to petition]
A White House statement on behalf of the President Obama said: "Thank you for taking the time to sign on to this petition in support of banning the practice known as conversion therapy.
"Often, this practice is used on minors, who lack the legal authority to make their own medical and mental health decisions.
"We share your concern about its potentially devastating effects on the lives of transgender as well as gay, lesbian, bisexual, and queer youth.
"The overwhelming scientific evidence demonstrates that conversion therapy, especially when it is practiced on young people, is neither medically nor ethically appropriate and can cause substantial harm.
"As part of our dedication to protecting America's youth, this Administration supports efforts to ban the use of conversion therapy for minors."
"Thank you for taking the time to sign on to this petition in support of banning the practice known as conversion therapy.
In a suicide note left on the social media site Tumblr, Leelah Alcorn said: "Even if you are Christian or are against transgender people don't ever say that to someone, especially your kid. That won't do anything but make them hate them self. That's exactly what it did to me.
"The only way I will rest in peace is if one day transgender people aren't treated the way I was... My death needs to mean something. Fix society. Please."
A number of Christian groups claim the therapy is vital for those who believe God's plan is for heterosexual relationships only.
Speaking in response to calls in the UK for the therapy to be banned, Andrew Symes from Anglican Mainstream said: "Currently anyone with same sex attraction has freedom of choice to do one of three things: to embrace "gay" identity and enter into a homosexual relationship or relationships; to live with the feelings but resist the temptation to act on them and live a life of celibacy, or to seek to reduce the feelings and develop heterosexual attraction, perhaps with a view to marriage and family.
"The Bill seeks to deny the latter of the three choices, thus creating a major and completely unnecessary restriction on human liberty. It is also a threat to religious freedom: the right for a person not just to believe in Christ, but to seek help in following him in every area of life."