The Irish musician received the magazine's first Man of the Year award at the star-studded ceremony in Los Angeles.
On stage, Bono said: “I know how ridiculous it is for me to be on this stage accepting this award. But if I didn't know how ridiculous it was, I did have the blessed internet to remind me.
“As my daughter Jordan says, there is nowhere on earth where women have the same opportunities as men.
“Unless we address this problem, both men and women together, the world will continue down this misogynistic, violent and impoverished path.
“I say to the president-elect: look across to women, make equality a priority, it is the only way forward.
“The train is leaving the station, be on it or be under it.”
He was recognised after his One campaign launched a “Poverty is Sexist” movement last year.
In a letter to world leaders, Bono and a host of celebrities including Sir Elton John, Robert Redford and Oprah Winfrey called it an outrage that girls account for 74% of all new HIV infections among adolescents in Africa.
At the awards ceremony, actress Amber Heard read the victim impact statement of the survivor of the Stanford sexual assault case, known only as Emily Doe.
The poignant letter went viral earlier this year amid criticism of the six-month sentence handed to former Olympic swimming hopeful Brock Turner for sexually assaulting an unconscious woman at the US university campus. He was released in September after serving half of his term.
Heard, whose high-profile divorce battle with Johnny Depp involved allegations of domestic abuse, joined fellow actresses Gabourey Sidibe and Freida Pinto on stage to read the letter.
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