The article in Attitude magazine marks the first time a British royal has been photographed for the cover of a gay publication, the magazine said.
The cover features a smiling Duke of Cambridge wearing an open-necked shirt, along with a quote from the future British king: "No one should be bullied for their sexuality or any other reason."
The article came about after William invited the publication to bring lesbian, gay, bisexual and transgender people to Kensington Palace to share their experiences on bullying, a statement from Attitude said.
The magazine's editor, Matthew Todd, facilitated the discussion during which participants spoke about the struggles they've dealt with, including suicide attempts, depression, drug addiction and eating disorders.
The prince then posed for the cover, shot by photographer Leigh Keily.
"No one should be bullied for their sexuality or any other reason and no one should have to put up with the kind of hate that these young people have endured in their lives," Prince William said in a statement.
"The young gay, lesbian and transgender individuals I met through Attitude are truly brave to speak out and to give hope to people who are going through terrible bullying right now. Their sense of strength and optimism should give us all encouragement to stand up to bullying wherever we see it," he added.
Bullying 'must stop'
Todd, the magazine's editor, said he met parents who had lost their children to suicide after being bullied for their sexuality.
"I am very happy that the future King of the United Kingdom agrees this must stop and I would urge parents in particular to raise their voices in their communities to ensure that every school protects -- really protects -- all children."
A Kensington Palace spokesman said: "The Duke of Cambridge is working hard to support the fight against bullying and to help break the stigma around mental health. He has established a task force on the prevention of cyberbullying and along with the Duchess of Cambridge and Prince Harry is leading the Heads Together campaign on mental health and well-being."
The news was announced the day after the Duke and Duchess of Cambridge signed a condolence book at the U.S. Embassy in London for victims of the terror attack on a gay nightclub in Orlando, Florida.
Founded in 1994, Attitude bills itself as the UK's best-selling gay magazine, and has featured such celebrities on its cover as Daniel Radcliffe, David Beckham, Lady Gaga and James Franco.
The digital version of the magazine is available now, while the print edition will be out in the UK on June 22, said Mike Buckley, Attitude's managing director.